Difference between revisions of "NCBI"

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[http://www.ncbi.nlm.nih.gov/ NCBI] is the National Center for Biotechnology Information. Various sequence file formats have developed for submission into public databases housed at NCBI in [http://www.insdc.org/page.php?page=home collaboration] with [http://www.ebi.ac.uk/embl/ EBML] and [http://www.ddbj.nig.ac.jp/ DDBJ].
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==Genbank format==
 
Genbank is a publicly accessible flat file database structure for primary nucleotide sequence information and auxillary information. The amount of information publically submitted has been growing exponentially. In August 2005 this DNA sequence database reached 100 gigabases. The structure of the record is reasonably consise, each field is a key-value pair where the value information can be quite flexible depending on the key, for example these records can display the [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#OriginB ORIGIN] information for different nucleotide molecular types, and have no limit on the length of sequence displayed. Entire chromosomes can be stored as a genbank record for an organism of interest, potentially making the disk storage of the record very large. There is one key which displays Information about genes and gene products that is extremely flexible (the FEATURE table), this is because it is made up of optional ''features'' which have optional key=value pair qualifiers nested within them.
 
Genbank is a publicly accessible flat file database structure for primary nucleotide sequence information and auxillary information. The amount of information publically submitted has been growing exponentially. In August 2005 this DNA sequence database reached 100 gigabases. The structure of the record is reasonably consise, each field is a key-value pair where the value information can be quite flexible depending on the key, for example these records can display the [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#OriginB ORIGIN] information for different nucleotide molecular types, and have no limit on the length of sequence displayed. Entire chromosomes can be stored as a genbank record for an organism of interest, potentially making the disk storage of the record very large. There is one key which displays Information about genes and gene products that is extremely flexible (the FEATURE table), this is because it is made up of optional ''features'' which have optional key=value pair qualifiers nested within them.
  
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An example Genbank [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html sample record] ''([http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=1293613 U49845 actual Genbank record])''
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An example Genbank [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html sample record]  
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*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=1293613 U49845 actual Genbank record]
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*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=1293615 AAA98666 GenPept record]
  
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== Regular expressions matching parts we care about ==
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Content of interest include all the linkout associations in the examples above;
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===Genbank===
 
 
*The unique [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#AccessionB ACCESSION] number
 
*The unique [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#AccessionB ACCESSION] number
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*Any amino acid [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#TranslationB /translation] field in the [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#FeaturesB FEATURE] table
 
*The ORIGIN field
 
*The ORIGIN field
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*Any amino acid [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#TranslationB /translation] field in the [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#FeaturesB FEATURE] table
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===See also===
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*[http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html Feature table definitions EBI]
  
 
===FASTA===
 
===FASTA===
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LAAVEAQQQMLKLTIWGVK
 
LAAVEAQQQMLKLTIWGVK
  
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''Note: Rendering of this FASTA file should really be in a monospaced font, where usually there is an 80 character limit in text before a newline''.
  
 
In the [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&qty=1&c_start=1&list_uids=1293613&uids=&dopt=fasta&dispmax=5&sendto=&fmt_mask=0&from=begin&to=end&extrafeatpresent=1&ef_CDD=8&ef_MGC=16&ef_HPRD=32&ef_STS=64&ef_tRNA=128&ef_microRNA=256 ''U49845 actual FASTA record''] the third field is ''gb'' which refers to the ''GENBANK ACCESSION'', a unique accession number. The fourth field is the GENBANK ACCESION number refering to the nucleotide GENBANK record.
 
In the [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&qty=1&c_start=1&list_uids=1293613&uids=&dopt=fasta&dispmax=5&sendto=&fmt_mask=0&from=begin&to=end&extrafeatpresent=1&ef_CDD=8&ef_MGC=16&ef_HPRD=32&ef_STS=64&ef_tRNA=128&ef_microRNA=256 ''U49845 actual FASTA record''] the third field is ''gb'' which refers to the ''GENBANK ACCESSION'', a unique accession number. The fourth field is the GENBANK ACCESION number refering to the nucleotide GENBANK record.
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;DNA example
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>gi|[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucest&qty=1&c_start=1&list_uids=33650851&uids=&dopt=gb&dispmax=5&sendto= 33650851]|gb|C81881.1|C81881 C81881 Citrus unshiu juice sac and pulp segment maturation stage Citrus unshiu cDNA clone pcMFrM02.04-023 5', mRNA sequence
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AGGTCAAGATTTGAGGAGAAAATGGGTTCTAGAGTAACACTTAGGACCAAAGGCAAGGGCGTGAAGGGAG
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CAAAGGCATCAGAGGAGAAATCAATGGTCGATTCTTTCAAAGAGTGGAGCACTTGGACCATGAAAAAGGC
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TAAAGTGGTCACTCACTATGGATTTATTCCTCTTATCATCATTTATCGGCATGAATTCTGATCCCAAGCC
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CCAAGTCTATCAGCTCCTCAGCCCCGTTTGATCTCCATACTTGACTCTTCCTTTTCTTTTGATGTCAAAC
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AAAATAGTTATTATCATGCTGTGCCTTCCTATTTGTCGAATCTACATGAATTGAATGTTTTAGGAGTTTT
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GGTTTCTTGTGATCGTACTTCCTGCCTAGTTGTAAGCTTATGGATTGACGTAGTATAAAATGTCTGGAAT
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TTGAATTATATACCGTCTCCATTGAATTGGAGGCNTCTTTTTCTTTTGGTGAATTTGTTTGTATTTTTTT
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TCCTTTTAGTTTCTTTGTTTACCATAGATCAATATTATAAGCATATTTTAATATT
  
 
==See also==
 
==See also==
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* [[Template:extension]] ''(template code constructor)''
 
* [[Template:extension]] ''(template code constructor)''
 
* [[Extension:Example]] ''(working example)''
 
* [[Extension:Example]] ''(working example)''
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* [http://en.wikipedia.org/wiki/Fasta_format Wikipedia FASTA]
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* [http://en.wikipedia.org/wiki/GenBank Wikipedia Genbank]

Latest revision as of 02:46, 23 April 2020

Legacy.svg Legacy: This article describes a concept that has been superseded in the course of ongoing development on the Organic Design wiki. Please do not develop this any further or base work on this concept, this is only useful for a historic record of work done. You may find a link to the currently used concept or function in this article, if not you can contact the author to find out what has taken the place of this legacy item.

NCBI is the National Center for Biotechnology Information. Various sequence file formats have developed for submission into public databases housed at NCBI in collaboration with EBML and DDBJ.

Genbank format

Genbank is a publicly accessible flat file database structure for primary nucleotide sequence information and auxillary information. The amount of information publically submitted has been growing exponentially. In August 2005 this DNA sequence database reached 100 gigabases. The structure of the record is reasonably consise, each field is a key-value pair where the value information can be quite flexible depending on the key, for example these records can display the ORIGIN information for different nucleotide molecular types, and have no limit on the length of sequence displayed. Entire chromosomes can be stored as a genbank record for an organism of interest, potentially making the disk storage of the record very large. There is one key which displays Information about genes and gene products that is extremely flexible (the FEATURE table), this is because it is made up of optional features which have optional key=value pair qualifiers nested within them.

An example Genbank sample record

Content of interest include all the linkout associations in the examples above;

See also

FASTA

There is a condensed file format called a FASTA format is used to manipulate primary sequence information. FASTA files can be nucleotide or amino acid records. the first row of the record starts with a > and can contain any description information about the record. It is recommended that all lines of text be shorter than 80 characters in length.

An example of an amino acid FASTA record, in this case the description information is a consise format separated by pipe characters |. The first field gi refers to GENBANK IDENTIFIER, a unique identification number. The second field is the GENBANK IDENTIFIER number refering to the amino acid GENPEPT record.


>gi|532319|pir|TVFV2E|TVFV2E envelope protein

ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT

QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC

HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK

MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK

TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF

APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL

LAAVEAQQQMLKLTIWGVK

Note: Rendering of this FASTA file should really be in a monospaced font, where usually there is an 80 character limit in text before a newline.

In the U49845 actual FASTA record the third field is gb which refers to the GENBANK ACCESSION, a unique accession number. The fourth field is the GENBANK ACCESION number refering to the nucleotide GENBANK record.

DNA example

>gi|33650851|gb|C81881.1|C81881 C81881 Citrus unshiu juice sac and pulp segment maturation stage Citrus unshiu cDNA clone pcMFrM02.04-023 5', mRNA sequence AGGTCAAGATTTGAGGAGAAAATGGGTTCTAGAGTAACACTTAGGACCAAAGGCAAGGGCGTGAAGGGAG CAAAGGCATCAGAGGAGAAATCAATGGTCGATTCTTTCAAAGAGTGGAGCACTTGGACCATGAAAAAGGC TAAAGTGGTCACTCACTATGGATTTATTCCTCTTATCATCATTTATCGGCATGAATTCTGATCCCAAGCC CCAAGTCTATCAGCTCCTCAGCCCCGTTTGATCTCCATACTTGACTCTTCCTTTTCTTTTGATGTCAAAC AAAATAGTTATTATCATGCTGTGCCTTCCTATTTGTCGAATCTACATGAATTGAATGTTTTAGGAGTTTT GGTTTCTTGTGATCGTACTTCCTGCCTAGTTGTAAGCTTATGGATTGACGTAGTATAAAATGTCTGGAAT TTGAATTATATACCGTCTCCATTGAATTGGAGGCNTCTTTTTCTTTTGGTGAATTTGTTTGTATTTTTTT TCCTTTTAGTTTCTTTGTTTACCATAGATCAATATTATAAGCATATTTTAATATT

See also

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