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Blast Database Sequences Length
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20 months 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!

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6.2 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!

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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...

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6.2 years ago
Pasta ♦ 1.3k
Switzerland

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.

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6.2 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.

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