Retrieve sequences in Tabulated Format

sequenceserver
#1

Hi Sequenceserver(ers),

Just wondering if anyone knows a way to retrieve the hits from the blast search in a tabulated format?
I’m working with 17 different assemblies as the genome quality isn’t great and need to create a “consensus contig” from the scaffolds.
This means sifting through a lot of hits each time…

Any ideas?

Thank you,

Luca.

#2

Hi Luca,

Thanks for your interest in seqserv. What you are asking sounds at least somewhat difficult - comparing assemblies isn’t easy. As for your specific question, currently seqserv doesn’t allow you to output tab delimited format, so you might have to resort to using the command line version of blast instead (-outfmt 6). You can still use the databases that were created with “seqsuenceserver format-databases”, however.

ben

#3

Dear Luca,

You can download tabular report using the new version of SequenceServer we announced recently - https://groups.google.com/forum/#!topic/sequenceserver/vuuRHmqg6YA.

– Priyam