Question: Blast command line
gravatar for doinelpierrot
8 weeks ago by
doinelpierrot10 wrote:

Hello all,

  • I would like to run a blastx on a fasta file in order to perform a quick functionnal annotation on swissprot.

  • So I ran succesfully :

    blastx -query "${QUERY}" -db "${BANK}" -out ${OUT_FILE} -max_target_seqs 1 ${BLAST_PARAM} -num_threads $NCPUS -outfmt "6 qseqid sseqid sacc pident length evalue bitscore"
  • However the output for my first line looks like this :

       TRINITY_DN80826_c0_g1_i1        PIAS1_HUMAN     PIAS1_HUMAN     58.879  107         2.52e-36        132

First don't understand why there is no hit accession in column 3 and : it is supposed to be given by the option sacc, and also there is one in blast web version !

Second, when I run web blast on web version I have as a result in description column :

RecName: Full=E3 SUMO-protein ligase PIAS1; AltName: Full=DEAD/H box-binding protein 1; AltName: Full=E3 SUMO-protein transferase PIAS1; AltName: Full=Gu-binding protein; Short=GBP; AltName: Full=Protein inhibitor of activated STAT protein 1; AltName: Full=RNA helicase II-binding protein [Homo sapiens]

How to have this information command line and not only a gene name like I do ?

Thank you for your help !

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by doinelpierrot10

Take a look at the options for -outfmt 6 and make changes to options you are adding. Full list of options is here.

ADD REPLYlink written 8 weeks ago by GenoMax95k

things like PIAS1_HUMAN are the swissprot accession IDs , so you actually got what you asked for. For more informative info do what @genomax said and change the output you request from the blast run (eg. use sallacc or the default output )

ADD REPLYlink written 8 weeks ago by lieven.sterck9.5k

I have tried sallacc and it gives me also the swissprot accession. Is there any way to also get the ncbi accession (for instance O75925 for PIAS1_HUMAN) ?

ADD REPLYlink written 8 weeks ago by doinelpierrot10

is that a DB you created yourself locally?

if so (and seeing that adding sallacc only returns the swissprot ID) it might be you did not format it correctly ...

ADD REPLYlink written 8 weeks ago by lieven.sterck9.5k

Does your db actually include such info? Maybe there's a map file you can later join with the blast output?

ADD REPLYlink written 8 weeks ago by 5heikki9.2k
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