SIM2GFF(1) General Commands Manual SIM2GFF(1)NAME
sim2gff - Converts SIM file into GFF formatted records
sim2gff [-frxyHh] sim_file > gff_file
This manual page documents briefly the sim2gff command.
sim2gff is a program written in Perl that converts SIM file into GFF formatted records (for use with gff2aplot and gff2javaplot).
OPTIONS -h, --help
Show summary of options.
-f Output is written to a file named <sim_file>.gff.
-r Interchange the order of sequences (Seq1 on y-axis, Seq2 on x-axis).
Specify the species name for species1 (default: "Seq1").
Specify the species name for species2 (default: "Seq2").
-H Use the fasta file headers for species labels.
The following perl-like exit status are returned:
1 Successful completion
SEE ALSO ali2gff(1), blat2gff(1), gff2aplot(1), parseblast(1).
sim2gff was written by Thomas Wiehe <email@example.com>.
This manual page was written by Nelson A. de Oliveira <firstname.lastname@example.org>, for the Debian project (but may be used by others).
Mon, 21 Mar 2005 21:44:15 -0300SIM2GFF(1)
Check Out this Related Man Page
WEIGHT(1) General Commands Manual WEIGHT(1)NAME
weight - calculates sequence weights for an alignment
weight [-options] <alignment file>
This manual page documents briefly the weight command.
weight is a program that calculates weights for a sequence alignment.
-b <f> Use BLOSUM weighting scheme at <f> fractional identity.
-f <f> Filter out seqs w/ fractional ident > <x> [0-1].
-h Help; print version and usage info.
Save weight-annotated alignment in <outfile>.
-p Use position based weight scheme (Henikoff & Henikoff).
-s <n> Sample <n> sequences at random into a new alignment.
-v Use Voronoi weight scheme (Sibbald & Argos).
Specify alignment file format <s>.
Allowed formats: SELEX, MSF, Clustal, a2m, PHYLIP.
Suppress verbose banner.
SEE ALSO afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1),
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
FAX : 1-314-362-2157
This manual page was written by Nelson A. de Oliveira <email@example.com>,
for the Debian project (but may be used by others).
Mon, 01 Aug 2005 15:28:08 -0300WEIGHT(1)
We have a mix of flavours of UNIX. Recently delegated to monitor all UNIX server from one single point of HP SIM.
HP-UX servers have been successfully brought under HP SIM and we have been getting hardware alerts and these have helped us take proactive steps.
Issue being faced is... (0 Replies)
I have an alignment file (.fasta) with ~80 sequences. They look like this-
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
I have two files: a.doc and b.txt
I wish to search the strings from file b.txt in a.doc and want to highlight them in a.doc with different colours using Perl or bash./awk/sed?
Please guide me. :)
Thanks!!!!! (10 Replies)
Hello, I am trying to concatenate two strings by merging the overlapped region. E.g.
Seq_merged=ACGTGCCCCCGTGTGTGTFunction strcat(char *dest, char *src) appends the src string to the dest string, ignoring the overlapped parts (prefix of src and suffix of dest).... (30 Replies)