Usage Of Format Specifiers For Blastx In Ncbi Standalone Blast

Question

[Raghul]

Hi to all I am doing blastx with ncbi standalone blast for large number of sequences. I am getting the output in outfmt -7 (tabular with comment lines). There are 'keywords' like frames/qframe/sframe which gives information about which ORF frame that gives the database hit. By default this information does not appear in output format 7. Can anybody tell me how to use this "keyword" to get 'frames' information in the output. I asked this question in ncbi-help before 4 days but I am yet to get a reply, May be they are thinking this could be a silly question (may be they could be right).

for more info see blastx -help in the ncbi standalone blast thank you raghul

I have give the specific portion of help section to see as below- Options 6, 7, and 10 can be additionally configured to produce a custom format specified by space delimited format specifiers. The supported format specifiers are: qseqid means Query Seq-id qgi means Query GI qacc means Query accesion sseqid means Subject Seq-id sallseqid means All subject Seq-id(s), separated by a ';' sgi means Subject GI sallgi means All subject GIs sacc means Subject accession sallacc means All subject accessions qstart means Start of alignment in query qend means End of alignment in query sstart means Start of alignment in subject send means End of alignment in subject qseq means Aligned part of query sequence sseq means Aligned part of subject sequence evalue means Expect value bitscore means Bit score score means Raw score length means Alignment length pident means Percentage of identical matches nident means Number of identical matches mismatch means Number of mismatches positive means Number of positive-scoring matches gapopen means Number of gap openings gaps means Total number of gaps ppos means Percentage of positive-scoring matches frames means Query and subject frames separated by a '/' qframe means Query frame sframe means Subject frame When not provided, the default value is: 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore', which is equivalent to the keyword 'std' Default = `0'

Answer 1

[Sujai Kumar]

Hi Raghul

You need a string that specifies the columns you want, enclosed in ' '. For example:

blastx -query FASTAFILE -db DBNAME -outfmt '7 std qframe sframe'

will give you tabular output with comments (7) with the "standard" 12 columns and the additional two columns qframe and sframe.

If you want to define your own columns, leave out the std:

-outfmt '7 qseqid qstart qend qlen qframe'

But I would recommend leaving the first 12 columns as they are and adding on extra columns at the end so that all scripts that rely on the first 12 columns being a certain way can continue to work.

• Sujai

[Raghul]

Thank you very much