Blast Database Sequences Length
3
0
Entering edit mode
12.2 years ago
Fungsten • 0

Hi all

I am doing blast queries using genomes as databases. I would like to know if is possible to filter out database sequences by their length. So, if there is a sequence in the database that is lesser than the query + several kb not use it. If this is not possible, there is a work arround to obtain the lengths of the sequences in the output?

Thanks!

blast database output • 4.8k views
ADD COMMENT
2
Entering edit mode
12.2 years ago
Nickengland ▴ 130

The length of the sequences is shown in the output. If you use XMLOutput it is there by default, if you use -outfmt 10 for csv format then you need to specify you want it with "slen" eg:

-outfmt "10 std slen"

see blastn --help for more options!

ADD COMMENT
0
Entering edit mode

I missed the custom output formatting options... That is what I need. I was also looking to the options of wu/ab-blast which I used sometimes and doesn't seem to have these ones. Thanks a lot, I will RTFM more carefully...

ADD REPLY
1
Entering edit mode
12.2 years ago
Pasta ★ 1.3k

If you are talking about the blast on the NCBI website, well you can you [slen] in the Entrez Query box. Check this link: Entrez Query

If you are using a local Blast DB, then just make a DB with sequences of the good length.

ADD COMMENT
1
Entering edit mode
12.2 years ago
Tyler Davis ▴ 20

ProteinLounge(http://www.proteinlounge.com/Tool/Tools.aspx) has a database that uses Blast called Clean Compare that may be helpful to you.

ADD COMMENT

Login before adding your answer.

Traffic: 2093 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6