| SEQNR(1e) | EMBOSS Manual for Debian | SEQNR(1e) |
NAME¶
seqnr - Removes redundancy from DHF files.
SYNOPSIS¶
seqnr -dhfinpath dirlist -dosing toggle -singletsdir directory -dosets toggle -insetsdir directory [-matrix matrixf] -mode list -thresh float -threshlow float -threshup float [-gapopen float] [-gapextend float] -dhfoutdir outdir -dored toggle -redoutdir outdir -logfile outfile
seqnr -help
DESCRIPTION¶
seqnr is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Utils:Database creation" command group(s).
OPTIONS¶
Input section¶
-dhfinpath dirlist
This option specifies the location of DHF files (domain
hits files) (input). A 'domain hits file' contains database hits (sequences)
with domain classification information, in the DHF format (FASTA or
EMBL-like). 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: ./
-dosing toggle
This option specifies whether to use singlet sequences
(e.g. DHF files) to filter input. Optionally, up to two further directories of
sequences may be read: these are considered in the redundancy calculation but
never appear in the output files. Default value: Y
-singletsdir directory
This option specifies the location of singlet filter
sequences (e.g. DHF files) (input). A 'domain hits file' contains database
hits (sequences) with domain classification information, in the DHF format
(FASTA or EMBL-like). 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: ./
-dosets toggle
This option specifies whether to use sets of sequences
(e.g. DHF files) to filter input. Optionally, up to two further directories of
sequences may be read: these are considered in the redundancy calculation but
never appear in the output files. Default value: Y
-insetsdir directory
This option specifies location of sets of filter
sequences (e.g. DAF files) (input). 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: ./
-matrix matrixf
This option specifies the residue substitution matrix
that is used for sequence comparison. Default value: EBLOSUM62
Required section¶
-mode list
This option specifies whether to remove redundancy at a
single threshold % sequence similarity or remove redundancy outside a range of
acceptable threshold % similarity. All permutations of pair-wise sequence
alignments are calculated for each set of input sequences in turn using the
EMBOSS implementation of the Needleman and Wunsch global alignment algorithm.
Redundant sequences are removed in one of two modes as follows: (i) If a pair
of proteins achieve greater than a threshold percentage sequence similarity
(specified by the user) the shortest sequence is discarded. (ii) If a pair of
proteins have a percentage sequence similarity that lies outside an acceptable
range (specified by the user) the shortest sequence is discarded. Default
value: 1
-thresh float
This option specifies the % sequence identity redundancy
threshold. The % sequence identity redundancy threshold determines the
redundancy calculation. If a pair of proteins achieve greater than this
threshold the shortest sequence is discarded. Default value: 95.0
-threshlow float
This option specifies the % sequence identity redundancy
threshold (lower limit). The % sequence identity redundancy threshold
determines the redundancy calculation. If a pair of proteins have a percentage
sequence similarity that lies outside an acceptable range the shortest
sequence is discarded. Default value: 30.0
-threshup float
This option specifies the % sequence identity redundancy
threshold (upper limit). The % sequence identity redundancy threshold
determines the redundancy calculation. If a pair of proteins have a percentage
sequence similarity that lies outside an acceptable range the shortest
sequence is discarded. Default value: 90.0
Additional section¶
-gapopen float
This option specifies the gap insertion penalty. The gap
insertion penalty is the score taken away when a gap is created. The best
value depends on the choice of comparison matrix. The default value assumes
you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL
matrix for nucleotide sequences. Default value: 10
-gapextend float
This option specifies the gap extension penalty. The gap
extension, penalty is added to the standard gap penalty for each base or
residue in the gap. This is how long gaps are penalized. Usually you will
expect a few long gaps rather than many short gaps, so the gap extension
penalty should be lower than the gap penalty. Default value: 0.5
Output section¶
-dhfoutdir outdir
This option specifies the location of DHF files (domain
hits files) of non-redundant sequences (output). A 'domain hits file' contains
database hits (sequences) with domain classification information, in the DHF
format (FASTA or EMBL-like). 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:
./
-dored toggle
This option specifies whether to retain redundant
sequences. If this option is set a DHF file (domain hits file) of redundant
sequences is written. Default value: N
-redoutdir outdir
This option specifies the location of DHF files (domain
hits files) of redundant sequences (output). A 'domain hits file' contains
database hits (sequences) with domain classification information, in the DHF
format (FASTA or EMBL-like). 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 SEQNR log file
(output). The log file contains messages about any errors arising while SEQNR
ran. Default value: seqnr.log
BUGS¶
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).
SEE ALSO¶
seqnr is fully documented via the tfm(1) system.
AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
COPYRIGHT¶
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.
| 08/11/2010 | DOMSEARCH 0.1.0++20100721 |