Bioinformatics resources

posted on 11:48 AM on Saturday 14 June 2008

NCBI Gene resource

This is a resource that I heavily use. Very useful as it allows one to operate on the gene as a unit instead of multiple individual dna sequences (some of which are incomplete). The following are some material which are useful on NCBI Gene.

• NCBI Handbook - this is a link to the relevant section on the NCBI Handbook.

• Gene Help - link to the help page for NCBI Gene. Very helpful resource especially for programmers.

• README - Gene readme file on the NCBI ftp site. Describes the various files available for download at the FTP site.
  Here are some searching tips (see Gene Help for more information):

• To search for a gene using a accession, use this search term accession[accn]].

• To limit by organism use this organism[orgn]].

• To limit to the symbol, use this symbol[sym]].

Standardized human gene names

Standardized human gene names at HGNC (HUGO Gene Nomenclature Committee) can be found here.

GFF

GFF is a frequently used file format for genome annotations. See here for the specifications. It is basically a tab delimited file with specific fields. Very simple to use.

Strange gene names

This is not a resource, just something interesting. Have a look at 20080614 0935 Interesting gene names for some interesting gene names.

BIND XML Parser

Click 20080614 1150 BIND XML Parser for a page on a BIND XML parser that I wrote.

PubMed search fields

Click here for the fields searchable in pubmed.

Enhancer Element Locator (EEL)

This is a good program to locate for transcriptional factor binding sites.

JASPAR Transcriptional Factor database

This is a good resource for motifs of transcriptional factors and it can be used by EEL.