Bioinformatics: Protein sequence databases names for use with BLAST

Bioinformatics: Protein sequence databases names for use with BLAST

In the "Nucleotide sequence databases names for use with BLAST" post, we've seen the nucleotide sequence databases names that we can use in a command line BLAST search, the same thing applies to Protein sequence databases when it come to use command line BLAST.

Here are some of the protein databases names that we can use with BLAST:

1- nr:  Non-redundant merge of SWISS-PROT, PIR, PRF, and proteins derived from GenBank coding sequences and PDB atomic coordinates

2- swissprot:  The SWISS-PROT database

3- pdb:  Amino acid sequences parsed from atomic coordinates of three-dimensional structures

4- ecoli:  All proteins encoded by the E. coli genome

5- yeast:  All proteins encoded by the S. cerevisiae genome

6- drosoph: All proteins encoded by the D. melanogaster genome

These are some of the abbreviations used in a commend line BLAST search, if you want more you can read the documentation of using command line BLAST on the internet.


As a Bioinformatician, learning to use command line BLAST on Linux is very important, because it will make parsing files and looking for specific info very easy, because what takes 1 minute in an automated task, will take half an our doing it by hand, and the number goes with the amount of data you want to retrieve.

Any questions, you're welcome:-).