Is it possible to download BLAT results as actual sequences i.e. in genbank or fasta format?

Question

[rmartson]

I need to be able to use BLAT like BLAST. I just want to put in a query and get back every result in aligned and complete fasta format. Is that even possible? Why does it seem so hard to work with?

[GenoMax]

get back every result in aligned and complete fasta format

Do you want the hits in fasta format or results in standard "blast" like (or blast columnar) format? Not feasible to do the former (directly) but certainly possible to do latter.

[rmartson]

I'm not very familiar with different formats but I just need the aligned sequences with 100bp upstream and downstream flanks. With BLAST output I can take the aligned sequences and then retrieve the 100bp flanks from the complete sequences if there are any.

What kind of format from BLAT would get me that information?

[GenoMax]

With BLAST output I can take the aligned sequences and then retrieve the 100bp flanks from the complete sequences if there are any.

Which blast output format are you referring to? Are you using the web interface at NCBI or some other utility to do that?

Blat is able to produce output in following formats when used on the command line:

-out=type      Controls output file format.  Type is one of:
                    psl - Default.  Tab-separated format, no sequence
                    pslx - Tab-separated format with sequence
                    axt - blastz-associated axt format
                    maf - multiz-associated maf format
                    sim4 - similar to sim4 format
                    wublast - similar to wublast format
                    blast - similar to NCBI blast format
                    blast8- NCBI blast tabular format
                    blast9 - NCBI blast tabular format with comments

[rmartson]

The NCBI web interface lets you download results in a variety of formats including fasta (aligned sequences), fasta (complete sequences) and genbank. I don't have any need to automate searches right now so I just carry them out using the web interface.

So it looks like I'll have to use pslx format there, though I'll need to figure out how to retrieve hit sequence with flanks from that.

Answer 1

[microfuge]

Not a direct answer by using browser but the command line utility gfClient from UCSC seems to do that. presuming the test.fa contains your input in fasta. The browser does outputs blast like alignments but one has to click on the blat output linke and I was unable to automate it. Presuming your genome is hg38 17781 is the port number. The servers and portnumbers can be obtained from the table blatServers in the hgcentral database.

gfClient -out=blast  blat1c.soe.ucsc.edu  17781 /gbdb/hg38 test.fa  output.txt

[rmartson]

Thanks I'll see what I can do