diff --git a/CURATED_SET/curated_service/add_h2bv_march2024.ipynb b/CURATED_SET/curated_service/add_h2bv_march2024.ipynb new file mode 100644 index 00000000..aa655522 --- /dev/null +++ b/CURATED_SET/curated_service/add_h2bv_march2024.ipynb @@ -0,0 +1,1209 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/mnt/scratch/l_singh/hdb/project_dir/histonedb/CURATED_SET\n" + ] + } + ], + "source": [ + "%cd '..'" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "import inspect\n", + "import os\n", + "import re\n", + "import sys\n", + "\n", + "import pandas as pd\n", + "from Bio import Entrez, SeqIO\n", + "from curated_set_services import CuratedSet" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "((561, 16),\n", + " Index(['accession', 'type', 'variant_group', 'variant', 'doublet', 'gi',\n", + " 'ncbi_gene_id', 'hgnc_gene_name', 'taxonomy_id', 'organism', 'phylum',\n", + " 'class', 'taxonomy_group', 'info', 'references', 'sequence'],\n", + " dtype='object'))" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Load data from histones.csv\n", + "curated_set = CuratedSet()\n", + "cs = curated_set\n", + "\n", + "cs.data.shape, cs.data.columns" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "list(cs.has_duplicates())" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
accessiontypevariant_groupvariantdoubletgincbi_gene_idhgnc_gene_nametaxonomy_idorganismphylumclasstaxonomy_groupinforeferencessequence
\n", + "
" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [accession, type, variant_group, variant, doublet, gi, ncbi_gene_id, hgnc_gene_name, taxonomy_id, organism, phylum, class, taxonomy_group, info, references, sequence]\n", + "Index: []" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data[cs.data[\"accession\"] == \"AAO24603.1\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
accessiontypevariant_groupvariantdoubletgincbi_gene_idhgnc_gene_nametaxonomy_idorganismphylumclasstaxonomy_groupinforeferencessequence
NP_505463.1NP_505463.1H2AcH2AcH2A_(Animals)175620146239Caenorhabditis elegansNematodaChromadorea26989147 22650316(?)MSGRGKGGKAKTGGKAKSRSSRAGLQFPVGRLHRILRKGNYAQRVG...
EEC09557.1EEC09557.1H2AcH2AcH2A_(Animals)2155000636945Ixodes scapularisArthropodaArachnida26989147 22650316(?)MSGRGKGGKVKGKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAG...
NP_724343.1NP_724343.1H2AcH2AcH2A_(Animals)245856737227Drosophila melanogasterArthropodaInsecta26989147 22650316(?)MSGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAG...
XP_001119899.1XP_001119899.1H2AcH2AcH2A_(Animals)1107649357460Apis melliferaArthropodaInsecta26989147 22650316(?)MSGRGKGGKAKAKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAG...
EDO48405.1EDO48405.1H2AcH2AcH2A_(Animals)15622760245351Nematostella vectensisCnidariaAnthozoa26989147 22650316(?)MSGRGKGKAKGTKSKTRSSRAGLQFPVGRIHRHLRKGNYAERVGAG...
\n", + "
" + ], + "text/plain": [ + " accession type variant_group variant doublet \\\n", + "NP_505463.1 NP_505463.1 H2A cH2A cH2A_(Animals) \n", + "EEC09557.1 EEC09557.1 H2A cH2A cH2A_(Animals) \n", + "NP_724343.1 NP_724343.1 H2A cH2A cH2A_(Animals) \n", + "XP_001119899.1 XP_001119899.1 H2A cH2A cH2A_(Animals) \n", + "EDO48405.1 EDO48405.1 H2A cH2A cH2A_(Animals) \n", + "\n", + " gi ncbi_gene_id hgnc_gene_name taxonomy_id \\\n", + "NP_505463.1 17562014 6239 \n", + "EEC09557.1 215500063 6945 \n", + "NP_724343.1 24585673 7227 \n", + "XP_001119899.1 110764935 7460 \n", + "EDO48405.1 156227602 45351 \n", + "\n", + " organism phylum class \\\n", + "NP_505463.1 Caenorhabditis elegans Nematoda Chromadorea \n", + "EEC09557.1 Ixodes scapularis Arthropoda Arachnida \n", + "NP_724343.1 Drosophila melanogaster Arthropoda Insecta \n", + "XP_001119899.1 Apis mellifera Arthropoda Insecta \n", + "EDO48405.1 Nematostella vectensis Cnidaria Anthozoa \n", + "\n", + " taxonomy_group info references \\\n", + "NP_505463.1 26989147 22650316(?) \n", + "EEC09557.1 26989147 22650316(?) \n", + "NP_724343.1 26989147 22650316(?) \n", + "XP_001119899.1 26989147 22650316(?) \n", + "EDO48405.1 26989147 22650316(?) \n", + "\n", + " sequence \n", + "NP_505463.1 MSGRGKGGKAKTGGKAKSRSSRAGLQFPVGRLHRILRKGNYAQRVG... \n", + "EEC09557.1 MSGRGKGGKVKGKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAG... \n", + "NP_724343.1 MSGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAG... \n", + "XP_001119899.1 MSGRGKGGKAKAKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAG... \n", + "EDO48405.1 MSGRGKGKAKGTKSKTRSSRAGLQFPVGRIHRHLRKGNYAERVGAG... " + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(561, 16)" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "h2bv_accessions = [\n", + " \"AAO24603.1\",\n", + "]" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "((1, 5),\n", + " Index(['accession', 'type', 'variant_group', 'variant', 'references'], dtype='object'))" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df = pd.DataFrame(\n", + " {\n", + " \"accession\": h2bv_accessions,\n", + " \"type\": [\"H2B\"] * len(h2bv_accessions),\n", + " \"variant_group\": [\"H2B.V\"] * len(h2bv_accessions),\n", + " \"variant\": [\"H2B.V\"] * len(h2bv_accessions),\n", + " \"references\": [\"16303849\"] * len(h2bv_accessions),\n", + " }\n", + ")\n", + "df.index = df.accession\n", + "df.shape, df.columns" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
accessiontypevariant_groupvariantreferences
accession
AAO24603.1AAO24603.1H2BH2B.VH2B.V16303849
\n", + "
" + ], + "text/plain": [ + " accession type variant_group variant references\n", + "accession \n", + "AAO24603.1 AAO24603.1 H2B H2B.V H2B.V 16303849" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "((562, 16), [])" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data = pd.concat([cs.data, df]).fillna(\"\")\n", + "cs.data.shape, list(cs.has_duplicates())" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
accessiontypevariant_groupvariantdoubletgincbi_gene_idhgnc_gene_nametaxonomy_idorganismphylumclasstaxonomy_groupinforeferencessequence
NP_005312.1NP_005312.1H1H1.4H1.4_(Homo_sapiens)__???3008.0H1-49606Homo sapiensChordataMammaliaMammalia26689747MSETAPAAPAAPAPAEKTPVKKKARKSAGAAKRKASGPPVSELITK...
NP_005311.1NP_005311.1H1H1.3H1.3_(Homo_sapiens)__???3007.0H1-39606Homo sapiensChordataMammaliaMammalia26689747MSETAPLAPTIPAPAEKTPVKKKAKKAGATAGKRKASGPPVSELIT...
NP_006017.1NP_006017.1H1H1.10H1.10_(Homo_sapiens)__???8971.0H1-109606Homo sapiensChordataMammaliaMammalia26689747MSVELEEALPVTTAEGMAKKVTKAGGSAALSPSKKRKNSKKKNQPG...
NP_005309.1NP_005309.1H1H1.0H1.0_(Homo_sapiens)__???3005.0H1-09606Homo sapiensChordataMammaliaMammalia26689747MTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSS...
AAO24603.1AAO24603.1H2BH2B.VH2B.V16303849
\n", + "
" + ], + "text/plain": [ + " accession type variant_group variant \\\n", + "NP_005312.1 NP_005312.1 H1 H1.4 H1.4_(Homo_sapiens)__??? \n", + "NP_005311.1 NP_005311.1 H1 H1.3 H1.3_(Homo_sapiens)__??? \n", + "NP_006017.1 NP_006017.1 H1 H1.10 H1.10_(Homo_sapiens)__??? \n", + "NP_005309.1 NP_005309.1 H1 H1.0 H1.0_(Homo_sapiens)__??? \n", + "AAO24603.1 AAO24603.1 H2B H2B.V H2B.V \n", + "\n", + " doublet gi ncbi_gene_id hgnc_gene_name taxonomy_id organism \\\n", + "NP_005312.1 3008.0 H1-4 9606 Homo sapiens \n", + "NP_005311.1 3007.0 H1-3 9606 Homo sapiens \n", + "NP_006017.1 8971.0 H1-10 9606 Homo sapiens \n", + "NP_005309.1 3005.0 H1-0 9606 Homo sapiens \n", + "AAO24603.1 \n", + "\n", + " phylum class taxonomy_group info references \\\n", + "NP_005312.1 Chordata Mammalia Mammalia 26689747 \n", + "NP_005311.1 Chordata Mammalia Mammalia 26689747 \n", + "NP_006017.1 Chordata Mammalia Mammalia 26689747 \n", + "NP_005309.1 Chordata Mammalia Mammalia 26689747 \n", + "AAO24603.1 16303849 \n", + "\n", + " sequence \n", + "NP_005312.1 MSETAPAAPAAPAPAEKTPVKKKARKSAGAAKRKASGPPVSELITK... \n", + "NP_005311.1 MSETAPLAPTIPAPAEKTPVKKKAKKAGATAGKRKASGPPVSELIT... \n", + "NP_006017.1 MSVELEEALPVTTAEGMAKKVTKAGGSAALSPSKKRKNSKKKNQPG... \n", + "NP_005309.1 MTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSS... \n", + "AAO24603.1 " + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data.tail()" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(1, 16)" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data[cs.data[\"variant\"] == \"H2B.V\"].shape" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/l_singh/.conda/envs/histdb_env/lib/python3.8/site-packages/Bio/Entrez/__init__.py:658: UserWarning: \n", + "Email address is not specified.\n", + "\n", + "To make use of NCBI's E-utilities, NCBI requires you to specify your\n", + "email address with each request. As an example, if your email address\n", + "is A.N.Other@example.com, you can specify it as follows:\n", + " from Bio import Entrez\n", + " Entrez.email = 'A.N.Other@example.com'\n", + "In case of excessive usage of the E-utilities, NCBI will attempt to contact\n", + "a user at the email address provided before blocking access to the\n", + "E-utilities.\n", + " warnings.warn(\n", + "/home/l_singh/.conda/envs/histdb_env/lib/python3.8/site-packages/Bio/GenBank/__init__.py:1143: BiopythonParserWarning: Dropping bond qualifier in feature location\n", + " warnings.warn(\n", + "/mnt/scratch/l_singh/hdb/project_dir/histonedb/CURATED_SET/curated_set_services.py:267: SettingWithCopyWarning: \n", + "A value is trying to be set on a copy of a slice from a DataFrame.\n", + "Try using .loc[row_indexer,col_indexer] = value instead\n", + "\n", + "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", + " updating_data['accession'] = new_accessions\n" + ] + } + ], + "source": [ + "cs.update_accession_version()\n", + "cs.data = cs.data.set_index(cs.data.accession.values)" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(1, 16)" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data[cs.data[\"variant\"] == \"H2B.V\"].shape" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Fetched taxid from NCBI 5702\n", + " changes to 5702\n", + " changes to Trypanosoma brucei brucei\n", + " changes to Euglenozoa\n", + " changes to Kinetoplastea\n" + ] + } + ], + "source": [ + "curated_set.update_taxids(blank_data=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(1, 16)" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data[cs.data[\"variant\"] == \"H2B.V\"].shape" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
accessiontypevariant_groupvariantdoubletgincbi_gene_idhgnc_gene_nametaxonomy_idorganismphylumclasstaxonomy_groupinforeferencessequence
AAO24603.1AAO24603.1H2BH2B.VH2B.V5702Trypanosoma brucei bruceiEuglenozoaKinetoplastea16303849
\n", + "
" + ], + "text/plain": [ + " accession type variant_group variant doublet gi ncbi_gene_id \\\n", + "AAO24603.1 AAO24603.1 H2B H2B.V H2B.V \n", + "\n", + " hgnc_gene_name taxonomy_id organism phylum \\\n", + "AAO24603.1 5702 Trypanosoma brucei brucei Euglenozoa \n", + "\n", + " class taxonomy_group info references sequence \n", + "AAO24603.1 Kinetoplastea 16303849 " + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data[cs.data[\"variant\"] == \"H2B.V\"]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Updating sequences for H2B.V" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
accessiontypevariant_groupvariantdoubletgincbi_gene_idhgnc_gene_nametaxonomy_idorganismphylumclasstaxonomy_groupinforeferencessequence
AAO24603.1AAO24603.1H2BH2B.VH2B.V5702Trypanosoma brucei bruceiEuglenozoaKinetoplastea16303849
\n", + "
" + ], + "text/plain": [ + " accession type variant_group variant doublet gi ncbi_gene_id \\\n", + "AAO24603.1 AAO24603.1 H2B H2B.V H2B.V \n", + "\n", + " hgnc_gene_name taxonomy_id organism phylum \\\n", + "AAO24603.1 5702 Trypanosoma brucei brucei Euglenozoa \n", + "\n", + " class taxonomy_group info references sequence \n", + "AAO24603.1 Kinetoplastea 16303849 " + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data[cs.data['sequence'] == '']" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Downloading FASTA SeqRecords by ACCESSIONs from NCBI\n", + "Fetching 1 seqs\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/l_singh/.conda/envs/histdb_env/lib/python3.8/site-packages/Bio/Entrez/__init__.py:658: UserWarning: \n", + "Email address is not specified.\n", + "\n", + "To make use of NCBI's E-utilities, NCBI requires you to specify your\n", + "email address with each request. As an example, if your email address\n", + "is A.N.Other@example.com, you can specify it as follows:\n", + " from Bio import Entrez\n", + " Entrez.email = 'A.N.Other@example.com'\n", + "In case of excessive usage of the E-utilities, NCBI will attempt to contact\n", + "a user at the email address provided before blocking access to the\n", + "E-utilities.\n", + " warnings.warn(\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Sequence for AAO24603.1 changes from to MPPTKGGKRPLPLGGKGKGKRPPGQTTKSSSSRKKSGARRGKKQQRWDLYIHRTLRQVYKRGTLSKAAVRVLSSFIEDMYGKIQAEAVHVACINNVKTLTAREIQTSARLLLPPELAKHAMSEGTKAVAKYNASREEAYSKVL\n", + "Sequences updated: 1\n" + ] + } + ], + "source": [ + "cs.update_sequence(blank_data=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
accessiontypevariant_groupvariantdoubletgincbi_gene_idhgnc_gene_nametaxonomy_idorganismphylumclasstaxonomy_groupinforeferencessequence
AAO24603.1AAO24603.1H2BH2B.VH2B.V5702Trypanosoma brucei bruceiEuglenozoaKinetoplastea16303849MPPTKGGKRPLPLGGKGKGKRPPGQTTKSSSSRKKSGARRGKKQQR...
\n", + "
" + ], + "text/plain": [ + " accession type variant_group variant doublet gi ncbi_gene_id \\\n", + "AAO24603.1 AAO24603.1 H2B H2B.V H2B.V \n", + "\n", + " hgnc_gene_name taxonomy_id organism phylum \\\n", + "AAO24603.1 5702 Trypanosoma brucei brucei Euglenozoa \n", + "\n", + " class taxonomy_group info references \\\n", + "AAO24603.1 Kinetoplastea 16303849 \n", + "\n", + " sequence \n", + "AAO24603.1 MPPTKGGKRPLPLGGKGKGKRPPGQTTKSSSSRKKSGARRGKKQQR... " + ] + }, + "execution_count": 25, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cs.data[cs.data[\"variant\"] == \"H2B.V\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "sequence self \n", + " other MAPKAEKKPAAKKPAATPPPEEEKEVVPPPPAEKKPKAGKKLPAAK...\n", + "Name: CUT18447.1, dtype: object\n", + "sequence self \n", + " other AATPPPEEEKEVVPPPAEKKPAEKKPKAGKKLPASKEGDAKKKKKS...\n", + "Name: CUT18448.1, dtype: object\n", + "sequence self \n", + " other MAPKAEKKPAAKKPAATPPPEEEKEVVPPPPAEKKPKAGKKLPAAK...\n", + "Name: CUT18451.1, dtype: object\n", + "sequence self \n", + " other MPPRRKKTAAGAAAGGKAAAAAVGKAGFMPPKKPKKGKKKTPIMRY...\n", + "Name: CUT18449.1, dtype: object\n", + "sequence self \n", + " other MAPKSEKKPAEKKPVAEKPAAEEEKKSAPAPAAAEKKPAEKKPKAG...\n", + "Name: CUT18445.1, dtype: object\n", + "sequence self \n", + " other AEKKPKAGKKVPASKEGEKKKKRSKKSVETYKIYIFKVLKQVHPDI...\n", + "Name: CUT18446.1, dtype: object\n", + "sequence self \n", + " other MAPKSEKKPAEKKPVAEKPAAEEEKKAAPAAAPAEKKAAEKKPKA\n", + "Name: CUT18452.1, dtype: object\n", + "sequence self \n", + " other MAPKKKPSKLVGTVTKTRKVTETQTLKVSLTKGLKPEDQQTTTNKF...\n", + "Name: CUT18450.1, dtype: object\n", + "cp histones.csv backups/histones.csv-Mar0624163102\n", + "Previous data backuped to backups/histones.csv-Mar0624163102\n", + "Results saved to histones.csv\n" + ] + } + ], + "source": [ + "cs.save()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".conda-histdb_env", + "language": "python", + "name": "conda-env-.conda-histdb_env-py" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.1" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/CURATED_SET/histones.csv b/CURATED_SET/histones.csv index 04261d7b..76cf6fb7 100644 --- a/CURATED_SET/histones.csv +++ b/CURATED_SET/histones.csv @@ -388,6 +388,7 @@ XP_678689.1,H2B,H2B.Z,H2B.Z,,68073549,,,5823,Plasmodium berghei ANKA,Apicomplexa XP_001349046.1,H2B,H2B.Z,H2B.Z,,124511826,,,36329,Plasmodium falciparum 3D7,Apicomplexa,Aconoidasida,,,,MSGKGPAQKSQAAKKTAGKTLGPRHKRKRRTESFSLYIFKVLKQVHPETGVTKKSMNIMNSFINDIFDRLVTEATRLIRYNKKRTLSSREIQTAVRLLLPGELSKHAVSEGTKAVTKYTTSAA XP_002369740.1,H2B,H2B.Z,H2B.Z,,237840885,,,508771,Toxoplasma gondii ME49,Apicomplexa,Conoidasida,,,,MSGKGPAQKSQAAKKTAGKSLGPRYRRRKRTESFALYIYKVLKQVHPETGVSKKSMSIMNSFINDIFDRLADEAVRLIRYNKKRTLSSREIQTAVRLLLPGELSKHAVSEGTKAVTKYTTSGA HISTDB_H2B_Z_0,H2B,H2B.Z,H2B.Z,,,,,27996,Cytauxzoon felis,Apicomplexa,Aconoidasida,,,DOI:10.5772/intechopen.81409,MSGKVPSTKSQAAKKTAGKTLGVRYRRKKRIESFALYIYKVLKQVHPETGVSKKSMSIMNSFINDIFDRLALEATRLIRYNKKSTLSSREIQTAVRLLLPGELSKHAVSEGTKAVTKYTTSGV +AAO24603.1,H2B,H2B.V,H2B.V,,,,,5702,Trypanosoma brucei brucei,Euglenozoa,Kinetoplastea,,,16303849,MPPTKGGKRPLPLGGKGKGKRPPGQTTKSSSSRKKSGARRGKKQQRWDLYIHRTLRQVYKRGTLSKAAVRVLSSFIEDMYGKIQAEAVHVACINNVKTLTAREIQTSARLLLPPELAKHAMSEGTKAVAKYNASREEAYSKVL P02291.2,H2B,sperm_H2B_(Echinoidea),sperm_H2B_(Echinoidea),,108885304,,,7658,Parechinus angulosus,Echinodermata,Echinoidea,,,,MPRSPAKTSPRKGSPRKGSPSRKASPKRGGKGAKRAGKGGRRRRVVKRRRRRRESYGIYIYKVLKQVHPDTGISSRAMSVMNSFVNDVFERIAGEASRLTSANRRSTVSSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTTSR Q27749.3,H2B,sperm_H2B_(Echinoidea),sperm_H2B_(Echinoidea),,74767039,,,7660,Psammechinus miliaris,Echinodermata,Echinoidea,,,,MPSQKSPTKRSPTKRSPQKGGKGAKRGGKAGKRRRGVAVKRRRRRRESYGIYIYKVLKQVHPDTGISSRAMSVMNSFVNDVFERIASEAGRLTTYNRRNTVSSREVQTAVRLLLPGELAKHAVSEGTKAVTKYTTSR Q27750.3,H2B,sperm_H2B_(Echinoidea),sperm_H2B_(Echinoidea),,108860775,,,7660,Psammechinus miliaris,Echinodermata,Echinoidea,,,,MPKSPSKSSPRKGSPRKGSPRKGSPKRGGKGAKRAGKGGRRNVVKRRRRRRESYGIYIYKVLKQVHPDTGISSRGMSVMNSFVNDVFERIAGEASRLTSANRRSTISSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTTARR @@ -450,9 +451,14 @@ XP_006969783.1,H3,H3.3,H3.3,,589115521,,,431241,Trichoderma reesei QM6a,Ascomyco NP_009564.1,H3,H3.3,H3.3,,6319482,,,559292,Saccharomyces cerevisiae S288C,Ascomycota,Saccharomycetes,,,,MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGERS NP_002098.1,H3,H3.3,H3.3_(Homo_sapiens),,,3020.0,H3-3A,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,19412883,MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA NP_005315.1,H3,H3.3,H3.3_(Homo_sapiens),,,3021.0,H3-3B,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,19412883,MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA -NP_001013721.2,H3,H3.5,H3.5_(Homo_sapiens)__???,,,440093.0,H3-5,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,21274551,MARTKQTARKSTGGKAPRKQLATKAARKSTPSTCGVKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFNTDLRFQSAAVGALQEASEAYLVGLLEDTNLCAIHAKRVTIMPKDIQLARRIRGERA -NP_001342338.1,H3,H3.7(?),H3.7(?)_(Homo_sapiens)__???,,,440686.0,H3-7,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,12408966,MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQEFKTDLRFQSSAVMALQEAREAYLVGLFEDTNLCAIHAKRVTIMPKDIQLVSRIRGERA -XP_003804825.1,H3,TS_H3.4,TS_H3.4__???,,397466137,,,9597,Pan paniscus,Chordata,Mammalia,,,,MARTKQTARKSTGGKAPRKQLVTKVARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLMREIAQDFKTDLRFQSSAVMALQEACESYLVGLFEDTNLCVIHAKRVTIMPKDIQLARRIRGERA +NP_001358848.1,H3,H3.Y,H3.Y.2_(Homo_sapiens)__???,,,340096.0,H3Y2,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,20819935,MARTKQTARKATAWQAPRKPLATKAARKRASPTGGIKKPHRYKPGTLALREIRKYQKSTQLLLRKLPFQRLVREIAQAISPDLRFQSAAIGALQEASEAYLVQLFEDTNLCAIHARRVTIMPRDMQLARRLRGEGAGEPTLLGNLAL +XP_003954426.1,H3,H3.5,H3.5__???,,410046862,,,9598,Pan troglodytes,Chordata,Mammalia,,,,MARTKQTARKSTGGKAPRKQLATKAARKSTPSTXGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFNTDLRFQSAAVGALQEASEAYLVGLLEDTNLCAIHAKRVTIMPKDIQLARRIRGERA +HISTDB_H3_Y_0,H3,H3.Y,H3.Y__???,,NOGI,,,9544,Macaca mulatta,Chordata,Mammalia,,,,ARTKQTARKATNWQAPRKPLATKAAAKRAPPRGGIKKPHRYKPGTQALREIRKYQKSTQLLLRKLPFQCLVREIAQVISLDLRFQSAAIGALQEASEAYLVNLFEDTNLCAIHARRVTIMPRDMQLARRIRGEGAXEPTLLGNVAL +HISTDB_H3_Y_1,H3,H3.Y,H3.Y__???,,NOGI,,,9544,Macaca mulatta,Chordata,Mammalia,,,,ARTKQTARKATNWQAPRKPLATKAPGKRLPPRGGIKKPHRYRPGTQALREIRKYQKSTQLLLRKLPFQRLVREIAQAISPDLRFQSAAIGALQEASEAYLVNLFEDTNLCAIHARRVTIMPRDMQLARRIRGEGA +HISTDB_H3_Y_2,H3,H3.Y,H3.Y__???,,NOGI,,,9598,Pan troglodytes,Chordata,Mammalia,,,,ARTKQTARKATAWQAPRKPLATKAAGKRAPPTGGIKKPHRYKPGTLALREIRKYQKSTQLLLRKLPFQRLVREIAQAISPDLRFQSAAIGALQEASEAYLVQLFEDTNLCAIHARRVTIMPRDMQLARRLRREGP +HISTDB_H3_Y_3,H3,H3.Y,H3.Y__???,,NOGI,,,9598,Pan troglodytes,Chordata,Mammalia,,,,ARTKQTARKATAWQAPRKPLATKAARKRASPTGGIKKPHRYKPGTLALREIRKYQKSTQLLLRKLPFQRLVREIAQAISLDLRFQSAAIGALQEASEAYLVQLFEDTNLCAIHARRVTIMPQDMQLARRLRGEGAREPTLLGNLAL +NP_001800.1,H3,cenH3,cenH3_(Homo_sapiens)__???,,,1058.0,CENPA,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,23324462,MGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEEGLG +NP_001035891.1,H3,cenH3,cenH3_(Homo_sapiens)__???,,,1058.0,CENPA,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,23324462,MGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKSTHLLIRKLPFSRLAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEEGLG NP_563627.1,H3,cenH3,cenH3__???,,18378832,,,3702,Arabidopsis thaliana,Streptophyta,Magnoliopsida,,,,MARTKHRVTRSQPRNQTDAAGASSSQAAGPTTTPTRRGGEGGDNTQQTNPTTSPATGTRRGAKRSRQAMPRGSQKKSYRYRPGTVALKEIRHFQKQTNLLIPAASFIREVRSITHMLAPPQINRWTAEALVALQEAAEDYLVGLFSDSMLCAIHARRVTLMRKDFELARRLGGKGRPW NP_596473.1,H3,cenH3,cenH3__???,,19113265,,,4896,Schizosaccharomyces pombe,Ascomycota,Schizosaccharomycetes,,,,MAKKSLMAEPGDPIPRPRKKRYRPGTTALREIRKYQRSTDLLIQRLPFSRIVREISSEFVANFSTDVGLRWQSTALQCLQEAAEAFLVHLFEDTNLCAIHAKRVTIMQRDMQLARRIRGA NP_499128.1,H3,cenH3,cenH3__???,,17553736,,,6239,Caenorhabditis elegans,Nematoda,Chromadorea,,,,MADDTPIIEEIAEQNESVTRIMQRLKHDMQRVTSVPGFNTSAAGVNDLIDILNQYKKELEDDAANDYTEAHIHKIRLVTGKRNQYVLKLKQAEDEYHARKEQARRRASSMDFTVGRNSTNLVDYSHGRHHMPSYRRHDSSDEENYSMDGTNGDGNRAGPSNPDRGNRTGPSSSDRVRMRAGRNRVTKTRRYRPGQKALEEIRKYQKTEDLLIQKAPFARLVREIMQTSTPFGADCRIRSDAISALQEAAEAFLVEMFEGSSLISTHAKRVTLMTTDIQLYRRLCLRHL @@ -466,16 +472,11 @@ XP_002287626.1,H3,cenH3,cenH3__???,,223995905,,,296543,Thalassiosira pseudonana XP_001011273.1,H3,cenH3,cenH3__???,,118356028,,,312017,Tetrahymena thermophila SB210,Ciliophora,Oligohymenophorea,,,,MARKAYQPKRRSNSNQNQQRSDSLKKNKQDNLRSKSAGNQQGNEKNKKDIQDQRNKASTKKKRESSGEKYESARDKVIRRFRPGDNALKQLRQYNQTPSLLIRKLPFQRLIREISTRMTEEDSLRWTSFALVLLQTVVEDYMVSFFEDANACALHAKRVTLMSKDLALAARIRGQKNVTGIFIPTKK XP_002767160.1,H3,cenH3,cenH3__???,,294874934,,,423536,Perkinsus marinus ATCC 50983,Perkinsozoa,None,,,,MVGVENLGVGFDELLTRGGCGVRDDAVEIAFRGVEGLEDVLKDYMVRNKDGKILSVARPVDAEHSEELLGLAAAIGRSYGSLICAAAHNGGVRLPVGKGDDDGDSNNSSDEEADSGCGGAAEGDEAGDVGAGAGDVGDGAGDGAAEGDGAGDAGNGAGDVGDVGDGAGDGAAEGDGAGDGAADDAHGAGDDGEGSRNGGPPLVVQMMVLVMMNGNGNGADDGGNGVDDGEGDGDGHQGNVEGDGHGDGQDDGDGEGSVDSSGNGGDSEPSLEVSREGSENRPKLLPPVEGRTSSSAAAIAAPPVPSAGSHIITGSGGKVPTAGKRPRQFVKKSSAKKGRYRPGTVALREIRRHQEITDPLIEKRCFQALARSLSREVEASMRWQPQSLVALQEASESFIVGMLEASQLLAVHGRRITLMEKDVKMWTRLAAMFGSTTFMDQEKQVGGT NP_012875.2,H3,cenH3,cenH3__???,,27808712,,,559292,Saccharomyces cerevisiae S288C,Ascomycota,Saccharomycetes,,,,MSSKQQWVSSAIQSDSSGRSLSNVNRLAGDQQSINDRALSLLQRTRATKNLFPRREERRRYESSKSDLDIETDYEDQAGNLEIETENEEEAEMETEVPAPVRTHSYALDRYVRQKRREKQRKQSLKRVEKKYTPSELALYEIRKYQRSTDLLISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLARRIRGQFI -HISTDB_H3_Y_0,H3,H3.Y,H3.Y__???,,NOGI,,,9544,Macaca mulatta,Chordata,Mammalia,,,,ARTKQTARKATNWQAPRKPLATKAAAKRAPPRGGIKKPHRYKPGTQALREIRKYQKSTQLLLRKLPFQCLVREIAQVISLDLRFQSAAIGALQEASEAYLVNLFEDTNLCAIHARRVTIMPRDMQLARRIRGEGAXEPTLLGNVAL -HISTDB_H3_Y_1,H3,H3.Y,H3.Y__???,,NOGI,,,9544,Macaca mulatta,Chordata,Mammalia,,,,ARTKQTARKATNWQAPRKPLATKAPGKRLPPRGGIKKPHRYRPGTQALREIRKYQKSTQLLLRKLPFQRLVREIAQAISPDLRFQSAAIGALQEASEAYLVNLFEDTNLCAIHARRVTIMPRDMQLARRIRGEGA -HISTDB_H3_Y_2,H3,H3.Y,H3.Y__???,,NOGI,,,9598,Pan troglodytes,Chordata,Mammalia,,,,ARTKQTARKATAWQAPRKPLATKAAGKRAPPTGGIKKPHRYKPGTLALREIRKYQKSTQLLLRKLPFQRLVREIAQAISPDLRFQSAAIGALQEASEAYLVQLFEDTNLCAIHARRVTIMPRDMQLARRLRREGP -HISTDB_H3_Y_3,H3,H3.Y,H3.Y__???,,NOGI,,,9598,Pan troglodytes,Chordata,Mammalia,,,,ARTKQTARKATAWQAPRKPLATKAARKRASPTGGIKKPHRYKPGTLALREIRKYQKSTQLLLRKLPFQRLVREIAQAISLDLRFQSAAIGALQEASEAYLVQLFEDTNLCAIHARRVTIMPQDMQLARRLRGEGAREPTLLGNLAL -NP_001342187.1,H3,H3.Y,H3.Y.1_(Homo_sapiens)__???,,,391769.0,H3Y1,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,20819935,MARTKQTARKATAWQAPRKPLATKAAGKRAPPTGGIKKPHRYKPGTLALREIRKYQKSTQLLLRKLPFQRLVREIAQAISPDLRFQSAAIGALQEASEAYLVQLFEDTNLCAIHARRVTIMPRDMQLARRLRREGP NP_003484.1,H3,H3.4,H3.4_(Homo_sapiens)__???,,,8290.0,H3-4,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,8986613,MARTKQTARKSTGGKAPRKQLATKVARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLMREIAQDFKTDLRFQSSAVMALQEACESYLVGLFEDTNLCVIHAKRVTIMPKDIQLARRIRGERA -NP_001358848.1,H3,H3.Y,H3.Y.2_(Homo_sapiens)__???,,,340096.0,H3Y2,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,20819935,MARTKQTARKATAWQAPRKPLATKAARKRASPTGGIKKPHRYKPGTLALREIRKYQKSTQLLLRKLPFQRLVREIAQAISPDLRFQSAAIGALQEASEAYLVQLFEDTNLCAIHARRVTIMPRDMQLARRLRGEGAGEPTLLGNLAL -XP_003954426.1,H3,H3.5,H3.5__???,,410046862,,,9598,Pan troglodytes,Chordata,Mammalia,,,,MARTKQTARKSTGGKAPRKQLATKAARKSTPSTXGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFNTDLRFQSAAVGALQEASEAYLVGLLEDTNLCAIHAKRVTIMPKDIQLARRIRGERA -NP_001800.1,H3,cenH3,cenH3_(Homo_sapiens)__???,,,1058.0,CENPA,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,23324462,MGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEEGLG -NP_001035891.1,H3,cenH3,cenH3_(Homo_sapiens)__???,,,1058.0,CENPA,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,23324462,MGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKSTHLLIRKLPFSRLAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEEGLG +NP_001013721.2,H3,H3.5,H3.5_(Homo_sapiens)__???,,,440093.0,H3-5,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,21274551,MARTKQTARKSTGGKAPRKQLATKAARKSTPSTCGVKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFNTDLRFQSAAVGALQEASEAYLVGLLEDTNLCAIHAKRVTIMPKDIQLARRIRGERA +XP_003804825.1,H3,TS_H3.4,TS_H3.4__???,,397466137,,,9597,Pan paniscus,Chordata,Mammalia,,,,MARTKQTARKSTGGKAPRKQLVTKVARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLMREIAQDFKTDLRFQSSAVMALQEACESYLVGLFEDTNLCVIHAKRVTIMPKDIQLARRIRGERA +NP_001342187.1,H3,H3.Y,H3.Y.1_(Homo_sapiens)__???,,,391769.0,H3Y1,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,20819935,MARTKQTARKATAWQAPRKPLATKAAGKRAPPTGGIKKPHRYKPGTLALREIRKYQKSTQLLLRKLPFQRLVREIAQAISPDLRFQSAAIGALQEASEAYLVQLFEDTNLCAIHARRVTIMPRDMQLARRLRREGP +NP_001342338.1,H3,H3.7(?),H3.7(?)_(Homo_sapiens)__???,,,440686.0,H3-7,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,12408966,MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQEFKTDLRFQSSAVMALQEAREAYLVGLFEDTNLCAIHAKRVTIMPKDIQLVSRIRGERA NP_180441.1,H4,cH4,cH4,,15226944,,,3702,Arabidopsis thaliana,Streptophyta,Magnoliopsida,,,,MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG NP_001131585.1,H4,cH4,cH4,,212722314,,,4577,Zea mays,Streptophyta,Magnoliopsida,,,,MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG NP_492641.1,H4,cH4,cH4,,17509199,,,6239,Caenorhabditis elegans,Nematoda,Chromadorea,,,,MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYCEHAKRKTVTAMDVVYALKRQGRTLYGFGG @@ -488,7 +489,6 @@ XP_012928609.2,H4,cH4,cH4,,861442511,,,10181,Heterocephalus glaber,Chordata,Mamm XP_951561.1,H4,cH4,cH4,,84043542,,,185431,Trypanosoma brucei brucei TREU927,Euglenozoa,Kinetoplastea,,,,MAKGKRVGESKGAQKRQKKVLRDNVRGITRGSIRRLARRAGVKRISGVIYDEVRGVLKTFVESIVRDAGAYTEYSRKKTVTAAHVVFALRKRGKVLYGYD XP_001016593.1,H4,cH4,cH4,,118366755,,,312017,Tetrahymena thermophila SB210,Ciliophora,Oligohymenophorea,,,,MAGGKGGKGMGKVGAKRHSRKSNKASIEGITKPAIRRLARRGGVKRISSFIYDDSRQVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG NP_009563.1,H4,cH4,cH4,,6319481,,,559292,Saccharomyces cerevisiae S288C,Ascomycota,Saccharomycetes,,,,MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG -NP_003538.1,H4,cH4(?),cH4(?)_(Homo_sapiens)__???,,,8369.0,H4C7,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,12408966,MSVRGKAGKGLGKGGAKCHRKVLSDNIQGITKCTIRRLARHGGVKRILGLIYEETRRVFKVFLENVIWYAVTNTEHAKRKTVTAMAVVYVLKRQGRTL NP_003529.1,H4,cH4,cH4_(Homo_sapiens)__???,,,8359.0,H4C1,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,12408966,MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG NP_003535.1,H4,cH4,cH4_(Homo_sapiens)__???,,,8366.0,H4C2,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,12408966,MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG NP_003533.1,H4,cH4,cH4_(Homo_sapiens)__???,,,8364.0,H4C3,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,12408966,MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG @@ -503,6 +503,7 @@ NP_003537.1,H4,cH4,cH4_(Homo_sapiens)__???,,,8368.0,H4C13,9606,Homo sapiens,Chor NP_003539.1,H4,cH4,cH4_(Homo_sapiens)__???,,,8370.0,H4C14,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,12408966,MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG NP_001029249.1,H4,cH4,cH4_(Homo_sapiens)__???,,,554313.0,H4C15,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,12408966,MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG NP_778224.1,H4,cH4,cH4_(Homo_sapiens)__???,,,121504.0,H4C16,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,12408966,MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG +NP_003538.1,H4,cH4(?),cH4(?)_(Homo_sapiens)__???,,,8369.0,H4C7,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,12408966,MSVRGKAGKGLGKGGAKCHRKVLSDNIQGITKCTIRRLARHGGVKRILGLIYEETRRVFKVFLENVIWYAVTNTEHAKRKTVTAMAVVYVLKRQGRTL NP_172161.1,H1,generic_H1,generic_H1,,15222199,,,3702,Arabidopsis thaliana,Streptophyta,Magnoliopsida,,,,MSEVEIENAATIEGNTAADAPVTDAAVEKKPAAKGRKTKNVKEVKEKKTVAAAPKKRTVSSHPTYEEMIKDAIVTLKERTGSSQYAIQKFIEEKRKELPPTFRKLLLLNLKRLVASGKLVKVKASFKLPSASAKASSPKAAAEKSAPAKKKPATVAVTKAKRKVAAASKAKKTIAVKPKTAAAKKVTAKAKAKPVPRATAAATKRKAVDAKPKAKARPAKAAKTAKVTSPAKKAVAATKKVATVATKKKTPVKKVVKPKTVKSPAKRASSRVKK P23444.2,H1,generic_H1,generic_H1,,121950,,,4577,Zea mays,Streptophyta,Magnoliopsida,,,,MATDVTETPAPLVDAAPEAPADAPAAPAADANAAKAKKATAPKKRASPTHLPYAEMVSEAITSLKERTGSSSYAIAKFVEDKHKAKLPPNFRKLLNVQLKKLVAGGKLTKVKNSYKLSSATKPNPKPKAAPKKPKTGAKKPKAAAKPKAKTPAKAKPATKPKPAAKPKAVVKPKTPAKPKAKPAAKAKPKTAGAKPKPLAKKAGRAKAAKTSAKDTPGKKAPAKKAAPSKKAATPVRKAPSRKAKK O17536.3,H1,generic_H1,generic_H1,,54035964,,,6239,Caenorhabditis elegans,Nematoda,Chromadorea,,,,MSDVAVAADTTETPAAPTKASKATKASKATKASKATKAKTTKVPMVKADAAHPPFINMVTEAISSIKDRKGPSRAAILKYITTKYTLGDQANKINAHLRKALNKGLESNAFVQASGNGANGRFRLAEKTASVAKSPAAAKKDATGEKKATTTVAKKAATGEKKATTTVAKKAATGEKKATTTVAKKAAAGDKAKKTEVKVKKVKSPKKIAKSPVNKVTKSPVKKIAKSSSMKAAPKKAAAKPAKKAPAAAPEA @@ -549,14 +550,14 @@ NP_001080265.1,H1,H1.10,H1.10,,147898445,,,8355,Xenopus laevis,Chordata,Amphibia ACO10502.1,H1,H1.10,H1.10,,225709312,,,217165,Caligus rogercresseyi,Arthropoda,Hexanauplia,,,,MVKSEVEVTINAEEAPVASSLKPAKKKKNKKKKNKPGKYSVLVLDAVKKLNERSGSSLVKIYNEAKKASWFDEQNGRTYLRYSIRALVLNNTLIQVKGMGANGSFRLNEDKFAKGVPKKTQSKPAKNTTKTAKASTTKKATVVKAKSSPKKAPDAKMPAAKLKKLGVKKVSAAQKNKKPKKASKPPAKSPRKK NP_015198.1,H1,scH1,scH1,,6325130,,,559292,Saccharomyces cerevisiae S288C,Ascomycota,Saccharomycetes,,,,MAPKKSTTKTTSKGKKPATSKGKEKSTSKAAIKKTTAKKEEASSKSYRELIIEGLTALKERKGSSRPALKKFIKENYPIVGSASNFDLYFNNAIKKGVEAGDFEQPKGPAGAVKLAKKKSPEVKKEKEVSPKPKQAATSVSATASKAKAASTKLAPKKVVKKKSPTVTAKKASSPSSLTYKEMILKSMPQLNDGKGSSRIVLKKYVKDTFSSKLKTSSNFDYLFNSAIKKCVENGELVQPKGPSGIIKLNKKKVKLST XP_011105792.1,H1,scH1,scH1,,748455219,,,1160507,Saccharomyces arboricola H-6,Ascomycota,Saccharomycetes,,,,MAPKKTSTKTTTTNKGKKPVTSKGKDKPVIKTAVKKNAAKKEEPSSKSYKELIVEGLAALKERKGSSRPALKKFIKENYPLVGSTSNFDLYFNNAIKKGVETGDFEQPKGPAGTLKLAKKKSPELKKETSPKPKQAAAATTTTTTTTPTSLKAKAKTASKKQAPKKVVKKKVPAVAVIPKKTSSPSALTYKEMILKSMPELNDGKGSSRIVLKKYVKDTFSSKLKTSSNFDYLFNSAIKKCVENGELVQPKGPSGIIKINKKKAKLST -NP_005311.1,H1,H1.3,H1.3_(Homo_sapiens)__???,,,3007.0,H1-3,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MSETAPLAPTIPAPAEKTPVKKKAKKAGATAGKRKASGPPVSELITKAVAASKERSGVSLAALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEGKPKAKKAGAAKPRKPAGAAKKPKKVAGAATPKKSIKKTPKKVKKPATAAGTKKVAKSAKKVKTPQPKKAAKSPAKAKAPKPKAAKPKSGKPKVTKAKKAAPKKK NP_861453.1,H1,H1.7,H1.7_(Homo_sapiens)__???,,,341567.0,H1-7,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MEQALTGEAQSRWPRRGGSGAMAEAPGPSGESRGHSATQLPAEKTVGGPSRGCSSSVLRVSQLVLQAISTHKGLTLAALKKELRNAGYEVRRKSGRHEAPRGQAKATLLRVSGSDAAGYFRVWKVPKPRRKPGRARQEEGTRAPWRTPAAPRSSRRRRQPLRKAARKAREVWRRNARAKAKANARARRTRRARPRAKEPPCARAKEEAGATAADEGRGQAVKEDTTPRSGKDKRRSSKPREEKQEPKKPAQRTIQ +NP_005314.2,H1,H1.6,H1.6_(Homo_sapiens)__???,,,3010.0,H1-6,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MSETVPAASASAGVAAMEKLPTKKRGRKPAGLISASRKVPNLSVSKLITEALSVSQERVGMSLVALKKALAAAGYDVEKNNSRIKLSLKSLVNKGILVQTRGTGASGSFKLSKKVIPKSTRSKAKKSVSAKTKKLVLSRDSKSPKTAKTNKRAKKPRATTPKTVRSGRKAKGAKGKQQQKSPVKARASKSKLTQHHEVNVRKATSKK +NP_005310.1,H1,H1.2,H1.2_(Homo_sapiens)__???,,,3006.0,H1-2,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MSETAPAAPAAAPPAEKAPVKKKAAKKAGGTPRKASGPPVSELITKAVAASKERSGVSLAALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKVKKAGGTKPKKPVGAAKKPKKAAGGATPKKSAKKTPKKAKKPAAATVTKKVAKSPKKAKVAKPKKAAKSAAKAVKPKAAKPKVVKPKKAAPKKK NP_005316.1,H1,H1.1,H1.1_(Homo_sapiens)__???,,,3024.0,H1-1,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MSETVPPAPAASAAPEKPLAGKKAKKPAKAAAASKKKPAGPSVSELIVQAASSSKERGGVSLAALKKALAAAGYDVEKNNSRIKLGIKSLVSKGTLVQTKGTGASGSFKLNKKASSVETKPGASKVATKTKATGASKKLKKATGASKKSVKTPKKAKKPAATRKSSKNPKKPKTVKPKKVAKSPAKAKAVKPKAAKARVTKPKTAKPKKAAPKKK NP_005313.1,H1,H1.5,H1.5_(Homo_sapiens)__???,,,3009.0,H1-5,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MSETAPAETATPAPVEKSPAKKKATKKAAGAGAAKRKATGPPVSELITKAVAASKERNGLSLAALKKALAAGGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKAKKAGAAKAKKPAGATPKKAKKAAGAKKAVKKTPKKAKKPAAAGVKKVAKSPKKAKAAAKPKKATKSPAKPKAVKPKAAKPKAAKPKAAKPKAAKAKKAAAKKK NP_722575.1,H1,H1.8,H1.8_(Homo_sapiens)__???,,,132243.0,H1-8,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MAPGSVTSDISPSSTSTAGSSRSPESEKPGPSHGGVPPGGPSHSSLPVGRRHPPVLRMVLEALQAGEQRRGTSVAAIKLYILHKYPTVDVLRFKYLLKQALATGMRRGLLARPLNSKARGATGSFKLVPKHKKKIQPRKMAPATAPRRAGEAKGKGPKKPSEAKEDPPNVGKVKKAAKRPAKVQKPPPKPGAATEKARKQGGAAKDTRAQSGEARKVPPKPDKAMRAPSSAGGLSRKAKAKGSRSSQGDAEAYRKTKAESKSSKPTASKVKNGAASPTKKKVVAKAKAPKAGQGPNTKAAAPAKGSGSKVVPAHLSRKTEAPKGPRKAGLPIKASSSKVSSQRAEA NP_001295191.1,H1,H1.8,H1.8_(Homo_sapiens)__???,,,132243.0,H1-8,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MAPATAPRRAGEAKGKGPKKPSEAKEDPPNVGKVKKAAKRPAKVQKPPPKPGAATEKARKQGGAAKDTRAQSGEARKVPPKPDKAMRAPSSAGGLSRKAKAKGSRSSQGDAEAYRKTKAESKSSKPTASKVKNGAASPTKKKVVAKAKAPKAGQGPNTKAAAPAKGSGSKVVPAHLSRKTEAPKGPRKAGLPIKASSSKVSSQRAEA NP_005312.1,H1,H1.4,H1.4_(Homo_sapiens)__???,,,3008.0,H1-4,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MSETAPAAPAAPAPAEKTPVKKKARKSAGAAKRKASGPPVSELITKAVAASKERSGVSLAALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKAKKAGAAKAKKPAGAAKKPKKATGAATPKKSAKKTPKKAKKPAAAAGAKKAKSPKKAKAAKPKKAPKSPAKAKAVKPKAAKPKTAKPKAAKPKKAAAKKK -NP_005309.1,H1,H1.0,H1.0_(Homo_sapiens)__???,,,3005.0,H1-0,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSSRQSIQKYIKSHYKVGENADSQIKLSIKRLVTTGVLKQTKGVGASGSFRLAKSDEPKKSVAFKKTKKEIKKVATPKKASKPKKAASKAPTKKPKATPVKKAKKKLAATPKKAKKPKTVKAKPVKASKPKKAKPVKPKAKSSAKRAGKKK -NP_005310.1,H1,H1.2,H1.2_(Homo_sapiens)__???,,,3006.0,H1-2,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MSETAPAAPAAAPPAEKAPVKKKAAKKAGGTPRKASGPPVSELITKAVAASKERSGVSLAALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKVKKAGGTKPKKPVGAAKKPKKAAGGATPKKSAKKTPKKAKKPAAATVTKKVAKSPKKAKVAKPKKAAKSAAKAVKPKAAKPKVVKPKKAAPKKK -NP_005314.2,H1,H1.6,H1.6_(Homo_sapiens)__???,,,3010.0,H1-6,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MSETVPAASASAGVAAMEKLPTKKRGRKPAGLISASRKVPNLSVSKLITEALSVSQERVGMSLVALKKALAAAGYDVEKNNSRIKLSLKSLVNKGILVQTRGTGASGSFKLSKKVIPKSTRSKAKKSVSAKTKKLVLSRDSKSPKTAKTNKRAKKPRATTPKTVRSGRKAKGAKGKQQQKSPVKARASKSKLTQHHEVNVRKATSKK +NP_005311.1,H1,H1.3,H1.3_(Homo_sapiens)__???,,,3007.0,H1-3,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MSETAPLAPTIPAPAEKTPVKKKAKKAGATAGKRKASGPPVSELITKAVAASKERSGVSLAALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEGKPKAKKAGAAKPRKPAGAAKKPKKVAGAATPKKSIKKTPKKVKKPATAAGTKKVAKSAKKVKTPQPKKAAKSPAKAKAPKPKAAKPKSGKPKVTKAKKAAPKKK NP_006017.1,H1,H1.10,H1.10_(Homo_sapiens)__???,,,8971.0,H1-10,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MSVELEEALPVTTAEGMAKKVTKAGGSAALSPSKKRKNSKKKNQPGKYSQLVVETIRRLGERNGSSLAKIYTEAKKVPWFDQQNGRTYLKYSIKALVQNDTLLQVKGTGANGSFKLNRKKLEGGGERRGAPAAATAPAPTAHKAKKAAPGAAGSRRADKKPARGQKPEQRSHKKGAGAKKDKGGKAKKTAAAGGKKVKKAAKPSVPKVPKGRK +NP_005309.1,H1,H1.0,H1.0_(Homo_sapiens)__???,,,3005.0,H1-0,9606,Homo sapiens,Chordata,Mammalia,Mammalia,,26689747,MTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSSRQSIQKYIKSHYKVGENADSQIKLSIKRLVTTGVLKQTKGVGASGSFRLAKSDEPKKSVAFKKTKKEIKKVATPKKASKPKKAASKAPTKKPKATPVKKAKKKLAATPKKAKKPKTVKAKPVKASKPKKAKPVKPKAKSSAKRAGKKK