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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Fungsten •
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!
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...
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.
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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