blastn use help

Question

[bibilong1111]

Hello!

I want to perform a blast search of splicing factors binding motifs on certain hg19 sequences defined by some grange objects generated by R. I find the splicing factor binding motifs on a website, and I download one of its page with the motif info.

http://193.206.120.249/splicing_tissue.html

http://193.206.120.249/cgi-bin/SpliceAid_Tissue_NewGraphics_SpliceSites.pl?sites=Download

I think it would be my database of sequences that my query sequences compared to. I tried to use it as a database but it is not working,how do I make it as a legit library for blastn? Thank you :)

The following is the command I'm using.

blastn -query seqs.fasta -out output.blast.txt -db /media/usb/data/splice_database/SpliceAid_Tissue_NewGraphics_SpliceSites.pl

Answer 1

[h.mon]

I think you have a long way before getting at what you want. First, you should help us help you by providing more information, for example, the error message BLAST gave. I also suspect you did not format a BLAST database with makeblastdb?

Anyway, it seems the download from the site you pointed is an html table, this is not suitable for further analyses and you have to parse the data. You need a fasta file to proceed.

Answer 2

[sunhanice]

Have you already indexed your database before the searching using the command like this?

makeblastdb -dbtype nucl -in input.fasta