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610 lines
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31 KiB
HTML
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<title>Human Genome Resources at NCBI - NCBI</title>
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<h1>Human Genome Resources at NCBI</h1>
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<ul>
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<li><a href="#download">Download</a></li>
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<li><a href="#find">Browse</a></li>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=4524"><img
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src="img/chromosomes/1.png" title="chromosome 1" alt="chromosome 1" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=3553" title="chromosome 2"><img
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src="img/chromosomes/2.png" alt="chromosome 2" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=9370" title="chromosome 3"><img
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src="img/chromosomes/3.png" alt="chromosome 3" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=4790" title="chromosome 4"><img
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src="img/chromosomes/4.png" alt="chromosome 4" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=7015" title="chromosome 5"><img
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src="img/chromosomes/5.png" alt="chromosome 5" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=7124" title="chromosome 6"><img
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src="img/chromosomes/6.png" alt="chromosome 6" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=1956" title="chromosome 7"><img
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src="img/chromosomes/7.png" alt="chromosome 7" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=4609" title="chromosome 8"><img
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src="img/chromosomes/8.png" alt="chromosome 8" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=1029" title="chromosome 9"><img
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src="img/chromosomes/9.png" alt="chromosome 9" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=5728" title="chromosome 10"><img
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src="img/chromosomes/10.png" alt="chromosome 10" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=627" title="chromosome 11"><img
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src="img/chromosomes/11.png" alt="chromosome 11" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=7421" title="chromosome 12"><img
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src="img/chromosomes/12.png" alt="chromosome 12" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=675" title="chromosome 13"><img
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src="img/chromosomes/13.png" alt="chromosome 13" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=3091" title="chromosome 14"><img
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src="img/chromosomes/14.png" alt="chromosome 14" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=1543" title="chromosome 15"><img
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src="img/chromosomes/15.png" alt="chromosome 15" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=999" title="chromosome 16"><img
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src="img/chromosomes/16.png" alt="chromosome 16" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=7157" title="chromosome 17"><img
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src="img/chromosomes/17.png" alt="chromosome 17" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=596" title="chromosome 18"><img
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src="img/chromosomes/18.png" alt="chromosome 18" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=348" title="chromosome 19"><img
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src="img/chromosomes/19.png" alt="chromosome 19" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=4318" title="chromosome 20"><img
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src="img/chromosomes/20.png" alt="chromosome 20" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=351" title="chromosome 21"><img
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src="img/chromosomes/21.png" alt="chromosome 21" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=1312" title="chromosome 22"><img
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src="img/chromosomes/22.png" alt="chromosome 22" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=367" title="chromosome X"><img
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src="img/chromosomes/x.png" alt="chromosome X" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=6736" title="chromosome Y"><img
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src="img/chromosomes/y.png" alt="chromosome Y" /></a>
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<a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=4512" title="MT"><img
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src="img/chromosomes/mt.png" alt="MT" /></a>
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<p class="small-font align-left">Select a chromosome to access the <a
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href="https://www.ncbi.nlm.nih.gov/genome/gdv/">Genome Data Viewer</a></p>
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<div class="clearfix"></div>
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<p><i class="fa fa-chevron-down fa-2x gray-icon"></i></p>
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</div>
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<div class="blue">
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<div id="download" class="usa-grid">
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<div class="resources usa-width-one-whole">
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<table class="usa-table-borderless">
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<thead>
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<tr>
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<th scope="col" class="blank">
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<h2>Download</h2>
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</th>
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<th scope="col">GRCh38</th>
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<th scope="col">GRCh37</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<th scope="row">
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Reference Genome Sequence
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</th>
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<td><a
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href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz"><button
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||
class="usa-button-outline" type="button">Fasta</button></a></td>
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||
<td><a
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||
href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.fna.gz"><button
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class="usa-button-outline" type="button">Fasta</button></a></td>
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</tr>
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<tr>
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<th scope="row">
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RefSeq Reference Genome Annotation
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</th>
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<td><a
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||
href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz"><button
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||
class="usa-button-outline" type="button">gff3</button></a></td>
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||
<td><a
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||
href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gff.gz"><button
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||
class="usa-button-outline" type="button">gff3</button></a></td>
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||
</tr>
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<tr>
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||
<th scope="row">
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RefSeq Transcripts
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</th>
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<td><a
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||
href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_rna.fna.gz"><button
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||
class="usa-button-outline" type="button">Fasta</button></a></td>
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||
<td><a
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||
href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_rna.fna.gz"><button
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||
class="usa-button-outline" type="button">Fasta</button></a></td>
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</tr>
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<tr>
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<th scope="row">
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RefSeq Proteins
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</th>
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<td><a
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href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_protein.faa.gz"><button
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||
class="usa-button-outline" type="button">Fasta</button></a></td>
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||
<td><a
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||
href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_protein.faa.gz"><button
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class="usa-button-outline" type="button">Fasta</button></a></td>
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</tr>
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<tr>
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<th scope="row">
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ClinVar
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</th>
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<td><a
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href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_clinvar.vcf.gz"><button
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||
class="usa-button-outline" type="button">vcf</button></a></td>
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||
<td><a
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||
href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_clinvar.vcf.gz"><button
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||
class="usa-button-outline" type="button">vcf</button></a></td>
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||
</tr>
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<th scope="row">
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dbSNP
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</th>
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<td><a
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href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_dbSNP_all.vcf.gz"><button
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||
class="usa-button-outline" type="button">vcf</button></a></td>
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||
<td><a
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||
href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_dbSNP_all.vcf.gz"><button
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||
class="usa-button-outline" type="button">vcf</button></a></td>
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||
</tr>
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<tr>
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||
<th scope="row">
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dbVar
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</th>
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<td><a
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||
href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_dbVar.gvf.gz"><button
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||
class="usa-button-outline" type="button">vcf</button></a></td>
|
||
<td><a
|
||
href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_dbVar.gvf.gz"><button
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||
class="usa-button-outline" type="button">vcf</button></a></td>
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||
</tr>
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||
</tbody>
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||
</table>
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||
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<p class="edirect">Do you want files preformatted for use in analysis pipelines?
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<a
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href=" https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p13/seqs_for_alignment_pipelines/">
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||
<button class="usa-button-outline" type="button">GRCh37</button></a>
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||
<a
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||
href="https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/">
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<button class="usa-button-outline" type="button">GRCh38</button></a>
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</p>
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<p class="edirect">Do you want programmatic access?
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<a href="https://github.com/NCBI-Hackathons/EDirectCookbook">
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||
<button class="usa-button-outline" type="button">EDirect Cookbook for Advanced
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||
users</button></a>
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||
</p>
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||
</div>
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||
</div>
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||
</div>
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||
|
||
<div id="find" class="usa-grid">
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||
<h2>Browse</h2>
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||
<div class="resources row">
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||
<div class="usa-width-one-third">
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||
<h3>Clinical & Variation Resources</h3>
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||
<ul class="usa-unstyled-list">
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||
<li><a href="https://www.ncbi.nlm.nih.gov/clinvar/">ClinVar
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<span>Information about genomic variation and its relationship to human
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health</span></a></li>
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<li><a href="https://www.ncbi.nlm.nih.gov/gtr/">Genetic Testing Registry (GTR)
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||
<span>Descriptions of genetic tests, submitted by test providers</span></a></li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/medgen/">MedGen
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||
<span>Information about medical conditions with a genetic
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||
contribution</span></a></li>
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||
<li><a href="https://ghr.nlm.nih.gov/">Genetics Home Reference
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||
<span>Consumer-friendly information about the effects of genetic variation on
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||
human health</span></a></li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/refseq/rsg/">RefSeqGene
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||
<span>Gene-focused genomic reference standard sequences that support reporting
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||
sequence variation</span></a></li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/snp/">dbSNP
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||
<span>Database of small-scale sequence variations</span></a></li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/dbvar/">dbVar
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<span>Database of genomic structural variation</span></a></li>
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</ul>
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||
</div>
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||
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||
<div class="usa-width-one-third">
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||
<h3>Assemblies & Annotations</h3>
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||
<ul class="usa-unstyled-list">
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||
<li><a href="https://genomereference.org">Genome Reference Consortium (GRC)
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||
<span>Information on assembly updates and issues from the international
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||
collaboration maintaining the human reference genome assembly</span></a>
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||
</li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/assembly/?term=human[organism]">Assembly
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||
<span>Human genome assemblies, organization, statistics, and
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||
meta-data</span></a></li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/genome/?term=human[organism]">Genome
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||
<span>Summary of genome-scale human data</span></a></li>
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||
<li><a
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||
href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=OGP__9606__9558">Blast
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||
Human
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||
<span>Align data to the human reference assembly, RefSeq, and more with
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||
BLAST</span></a></li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/gene/?term=human[organism]">Gene
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||
<span>Aggregated information about genes and genome annotation</span></a></li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/genome/tools/remap">NCBI Genome Remapping
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||
Service
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||
<span>Remap annotation data between different coordinate systems, including
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||
different assemblies and RefSeqGenes</span></a></li>
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||
</ul>
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||
</div>
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||
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||
<div class="usa-width-one-third">
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||
<h3>Related Resources</h3>
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||
<ul class="usa-unstyled-list">
|
||
<li><a href="https://www.ncbi.nlm.nih.gov/refseq/about/human/">RefSeq
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||
<span>Reference sequences for genomes, transcripts, proteins and more</span></a>
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||
</li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/sra/?term=human[organism]">Sequence Read
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||
Archive (SRA)
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||
<span>Human next generation sequence (NGS) transcriptome and genomic
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||
datasets</span></a></li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/gds/?term=human[organism]">GEO DataSets
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||
<span>Curated human gene expression datasets</span></a></li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/CCDS/">CCDS
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||
<span>Information on an international collaboration to consistently annotate
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||
human protein-coding genes</span></a></li>
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||
<li><a href="https://www.ncbi.nlm.nih.gov/books/NBK1116/">GeneReviews
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||
<span>An international point-of-care resource that provides clinically relevant
|
||
and medically actionable information for inherited conditions</span></a>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="blue usa-grid-full">
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<li><a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=4524">Genome Data
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Viewer
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<span>Browse and search a graphical view of the RefSeq annotated human reference
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genome</span></a></li>
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<li><a href="https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/">1000 Genomes
|
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<span>Explore variant calls, genotype calls and read alignments produced by
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the 1000 Genomes project</span></a></li>
|
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<li><a href="https://www.ncbi.nlm.nih.gov/variation/view/">Variation Viewer
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<span>View, search, and navigate variations housed in dbSNP, dbVar, and ClinVar
|
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alt="NCBI Human Variation and Medical Genetics Resources" />
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<span>Learn how to access resources associated with human sequence variations
|
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and phenotypes associated with specific human genes and
|
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phenotypes.</span></a></li>
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<li><a href="https://www.youtube.com/watch?v=cAh6-BALiT8">
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<img src="img/eukaryotic-genome-webinar.png"
|
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alt="Eukaryotic Genome Data Curation at NCBI" />
|
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<span>RefSeq biocurators focus on data curation for eukaryotic organisms,
|
||
including several aspects of manual curation like sequence analysis,
|
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functional annotation, data validation and community
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class="fa fa-video-camera" aria-hidden="true"></i> Genome Browser Tutorials
|
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<span><i>10 videos</i></span></a></li>
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<li><a href="https://www.youtube.com/playlist?list=PL76D7EE6A6A8AC1C3"><i
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class="fa fa-video-camera" aria-hidden="true"></i> Sequence Viewer Tutorials
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<span><i>13 videos</i> - Learn to use the Graphics display for NCBI sequence
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class="fa fa-video-camera" aria-hidden="true"></i> Genome Workbench
|
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Tutorials
|
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<span><i>10 videos</i> - NCBI's Genome Workbench for viewing and analysing
|
||
sequence data. It runs on your local machine.</span></a></li>
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<li><a href="ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_GRC.pdf"><i
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class="fa fa-file-text-o" aria-hidden="true"></i> Genome Reference
|
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Consortium (GRC)
|
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<span>Ensuring that the reference assemblies continue to grow as our
|
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understanding of these genomes evolve.</span></a></li>
|
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<li><a href="ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_Remap.pdf"><i
|
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class="fa fa-file-text-o" aria-hidden="true"></i> Genome Remapping Service
|
||
<span>A tool that makes remapping features and annotations simple and
|
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straightforward.</span></a></li>
|
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<li><a href="ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_ClinVar.pdf"><i
|
||
class="fa fa-file-text-o" aria-hidden="true"></i> ClinVar
|
||
<span>A public archive of the relationships between medically important variants
|
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and phenotypes. </span></a></li>
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<li><a href="ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_GTR.pdf"><i
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class="fa fa-file-text-o" aria-hidden="true"></i> Genetic Testing Registry
|
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(GTR)
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<span>A free online resource that provides centralized access to comprehensive
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class="fa fa-file-text-o" aria-hidden="true"></i> MedGen
|
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<span>MedGen provides up-to-date information about human disorders and other
|
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phenotypes with a genetic component.</span></a></li>
|
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<li><a href="ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_Genome.pdf"><i
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class="fa fa-file-text-o" aria-hidden="true"></i> Genome
|
||
<span>Organism-centered listing of available genomic sequence records and
|
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projects </span></a></li>
|
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<li><a href="ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_EukGenomeAnnotation.pdf"><i
|
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class="fa fa-file-text-o" aria-hidden="true"></i> Eukaryotic Genome
|
||
Annotation
|
||
<span>Organism-centered listing of available genomic sequence records and
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projects </span></a></li>
|
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<div class="usa-width-one-third">
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<ul class="usa-unstyled-list">
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class="fa fa-file-text-o" aria-hidden="true"></i> Reference Sequence
|
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Database (RefSeq)
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<span>Non-redundant genomic, RNA and protein sequence records, from microbes to
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class="fa fa-file-text-o" aria-hidden="true"></i> RefSeqGene
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<span>A collection of sequences as foundation for gene-based
|
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coordinates</span></a></li>
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<li><a href="ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_1000genomes_browser.pdf"><i
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class="fa fa-file-text-o" aria-hidden="true"></i> 1000 Genomes Browser
|
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|
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<li><a href="ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/Factsheet_Variation_Viewer.pdf"><i
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class="fa fa-file-text-o" aria-hidden="true"></i> Variation Viewer
|
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<span>A tool for interactive examination and download of nucleotide variants for
|
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|
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class="fa fa-file-text-o" aria-hidden="true"></i> Map Viewer
|
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<span>An online tool to view sequence- and marker-based genome maps in a single
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display </span></a></li>
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<h3>Related Links</h3>
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About the Human Genome Project</a></li>
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