What Program Or Database To Use To Analyze Blast Result Output?

Question

[Alby]

Hello, I ran the blast locally and got the blast output like following

query1 gi|4003386|dbj|AB020866.1|      98.44   64   1 ..   
query2 gi|60834728|gb|AY894071.1|      92.11   76   2 ...    
query3 gi|21618453|gb|BC032801.1|      92.11   76   6  ...

...

Now, is there way to retrieve human readable information from the data above?

For example, how can I map all gi|1619787|dbj|D85279.1|, gi|1619784|dbj|D85278.1| , gi|1619781|dbj|D85277.1| ... to corresponding genes? or is there a program available that allows you to analyze such output easily?

Thanks!

Answer 1

[Neilfws]

You're asking 2 questions here.

1. Can this BLAST output format be parsed to extract identifiers for the hits?
2. Can those identifiers be mapped to other information, such as gene names?

Answers:

1. Yes, very easily, in a multitude of ways. The output appears to be tab-delimited which makes it very easy to parse in the programming language of your choice. The identifiers, e.g. AB020866.1, are "pipe-delimited", so can easily be extracted.
2. Yes, one of several tools available online, such as BioMart or Gene ID converter.

To illustrate just one approach, GenBank identifiers can be extracted from the output using some basic UNIX tools:

cut -d "|" -f 4 blast.tab | sed 's/\.1//' > ids.txt

AB020866
AY894071 
BC032801
....

And both of the online tools mentioned previously return a gene name for one entry in that list of identifiers:

Ensembl Gene ID        Ensembl Transcript ID    HGNC symbol    EMBL (Genbank) ID
ENSG00000163586        ENST00000295834          FABP1          BC032801

[khikho]

Thanks for your info , But do you know how we can use their DB locally?! I mean I want to use their DB offline from terminal .

[Neilfws]

If you mean how to install BLAST databases locally, there are multiple guides online for doing that. Otherwise, post a new question (not in the comments).

[khikho]

No I mean install BioMart or Gene ID converter.

[Neilfws]

Why would you bother? The online services and their associated tools/APIs (e.g. the R biomaRt package) work just fine.