seqsearche - Online in the Cloud

PROGRAM:

NAME

seqsearch - Generate PSI-BLAST hits (DHF file) from a DAF file.

SYNOPSIS

seqsearch -mode list -inseqspath dirlist -database string -niter integer -evalue float
-maxhits integer -dhfoutdir outdir -logfile outfile

seqsearch -help

DESCRIPTION

seqsearch is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Protein:3D Structure" command group(s).

OPTIONS

Input section
-mode list
This option specifies the mode of SEQSEARCH operation. SEQSEARCH takes as input a
directory of either i. single sequences, ii. set of sequences (unaligned or aligned,
but typically aligned sequences within a domain alignment file)). The user has to
specify which. Default value: 1

-inseqspath dirlist
This option specifies the location of sequences, e.g. DAF files (domain alignment
files) (input). SEQSEARCH takes as input a database of either i. single sequences, ii.
sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment
file. A 'domain alignment file' contains a sequence alignment of domains belonging to
the same SCOP or CATH family. The file is in clustal format annotated with domain
family classification information. The files generated by using SCOPALIGN will contain
a structure-based sequence alignment of domains of known structure only. Such
alignments can be extended with sequence relatives (of unknown structure) by using
SEQALIGN. Default value: ./

-database string
Default value: swissprot

Required section
-niter integer
This option specifies the number of PSIBLAST iterations. This option specifies the
number of PSIBLAST iterations that are performed in a search. Default value: 1

-evalue float
This option specifies the threshold E-value for inclusion in family. This option
specifies the threshold E-value for a PSIBLAST hit to be retained. Default value:
0.001

-maxhits integer
This option specifies the maximum number of hits. This option specifies the maximum
number of PSIBLAST hit that are retained. It should normally be set high so that
nothing is discarded. Default value: 1000

Output section
-dhfoutdir outdir
This option specifies the location of DHF files (domain hits files) (output). A
'domain hits file' contains database hits (sequences) with domain classification
information, in FASTA format. The hits are relatives to a SCOP or CATH family and are
found from a search of a sequence database. Files containing hits retrieved by
PSIBLAST are generated by using SEQSEARCH. Default value: ./

-logfile outfile
This option specifies the name of log file for the build. The log file contains
messages about any errors arising while SEQSEARCH ran. Default value: seqsearch.log

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