Performing a BLAST of a BLAST result on web server

Question

[rikki.frederiksen]

Dear Biostars,

I am attempting to do use the BLAST web server for finding nucleotides which contain both of two query genes. I attempted to do a BLAST using the accession numbers of both genes separated with the logical operator AND. However, this lead to an error message. My second thought was to do a BLAST with one query gene, then followed by a second BLAST of these results using the second query gene. Is there someway I can either BLAST for the presence of both genes in nucleotides directly, or a way to do a BLAST of a previous BLAST result using the web server?

Best, Rikki

Answer 1

[GenoMax]

You can create a single file with the two sequences in it and blast with that one file. You will get results for both sequences in the output. You can look for hits that occur to both queries in the result. If you choose a column based output format (outfmt 6 or 7) then it may be easy to parse/sort the output to find this information.

[rikki.frederiksen]

Thanks Max. I forgot to mention that I am using the BLAST web server. I have edited the post accordingly. I will use BLAST+ instead and either apply your method, or use a custom database created from the first BLAST as database input in the second BLAST.

[GenoMax]

Even if you are using NCBI blast server you can still download the hits as a table. And then do an intersection of the two tables.