Difference between revisions of "NCBI"
(→FASTA: Fasta url) |
(→FASTA: gi, bg key value pairs: the definition) |
||
| Line 12: | Line 12: | ||
There is a condensed file format called a [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml 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. | There is a condensed file format called a [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml 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 second field is the | + | ''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.'' |
<pre> | <pre> | ||
>gi|[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=532319 532319]|pir|TVFV2E|TVFV2E envelope protein | >gi|[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=532319 532319]|pir|TVFV2E|TVFV2E envelope protein | ||
| Line 24: | Line 24: | ||
</pre> | </pre> | ||
| − | [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 '' | + | 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. |
==See also== | ==See also== | ||
Revision as of 10:40, 6 May 2007
Genbank is a publically 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. 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.
An example Genbank sample record (U49845 actual Genbank record)
Regular expressions matching parts we care about
Genbank
- The unique ACCESSION number
- The ORIGIN field
- Any amino acid /translation field in the FEATURE table
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|[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=532319 532319]|pir|TVFV2E|TVFV2E envelope protein ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL LAAVEAQQQMLKLTIWGVK
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.
See also
- NCBI GenBank Overview
- Template:extension (template code constructor)
- Extension:Example (working example)
