How to make blastp show complete gene name?
I download Swiss-prot protein in fasta format. The gene name is in this form
sp|Q5ANA3|CDR1_CANAL Pleiotropic ABC efflux transporter of multiple drugs CDR1 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) OX=237561 GN=CDR1 PE=1 SV=2
I want the "Pleiotropic ABC efflux transporter of multiple drugs CDR1 OS" to appear in the blastp output.
However when I ran
blastp -db ~/uniprot.fasta -query ~/CBS11016.genome.all.maker.proteins.fasta -out out.blastp -evalue .000001 -outfmt 6 -num_alignments 1 -seg yes -soft_masking true -show_gis -lcase_masking -max_hsps 1
The output is as seen below:
GEVV02003421.1 sp|Q59L89|SDHF3_CANAL 98.361 122 2 0 1 122 1 122 1.71e-85 242GEVV02003995.1 sp|Q59S27|RT106_CANAL 99.024 410 3 1 1 410 1 409 0.0 831
GEVV02006224.1 sp|Q59RL7|CPH2_CANAL 99.179 853 7 0 1 853 1 853 0.0 1729GEVV02000384.1 sp|Q6FNV5|HRD3_CANGA 29.960 247 131 6 63 271 97 339 1.47e-20 89.4
How can I make the output to show the full name?
2 answers
You can add additional columns in your Blast output:
Options 6, 7 and 10 can be additionally configured to produce a custom format specified by space delimited format specifiers, or by a token specified by the delim keyword. E.g.: "17 delim=@ qacc sacc score".
The delim keyword must appear after the numeric output format specification.
The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
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
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
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
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore', which is equivalent to the keyword 'std'
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It must exist a way to do this in the blast parameters, but i find it more easy to just
translatethe spaces to underlines (or other removable character like %):-outfmt '6 stitle <other column identifiers>'would get you tabular output withstitlebeing the column for the "full" name of the target.Hi, I had the same problem. And I plan to download a EXCEL format of the "header" in the SwissProt database and convert it into CSV.
grep the "SwissProt id found in blastp result" in the csv header file and get another result_header_file.
sort two files by the SwissProt id.
Then paste two files which are both delimited by comma.