stranslate(1) [debian man page]
STRANSLATE(1) General Commands Manual STRANSLATE(1) NAME
stranslate - translate a nucleic acid sequence to protein ORFs SYNOPSIS
stranslate [-options] <seqfile> DESCRIPTION
This manual page documents briefly the stranslate command. stranslate is a program that creates a file of all possible protein ORFs, given an input nucleic acid sequence. OPTIONS
Available options: -a Translate in full, with stops; no individual ORFs. -h Help; show brief usage and version info. -l <minlen> Report only ORFs greater than minlen (default 20). -m Require ORFs to start with AUG/Met. -o <outfile> Save results in output file. -q Quiet; silence banner, for piping or redirection. -s <stopchar> With -a, set stop character to <stopchar>. --tetrahymena Use the Tetrahymena/Oxytricha genetic code. --watson Only do the top strand (frames 0/1/2). --crick Only do the bottom strand (frames 3/4/5). NOTE TO DEBIAN USERS
The original program name is translate. It was renamed to stranslate to avoid conflict with another program of the same name. SEE ALSO
afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), weight(1). AUTHOR
Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others). Mon, 01 Aug 2005 15:28:08 -0300 STRANSLATE(1)
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COMPALIGN(1) General Commands Manual COMPALIGN(1) NAME
compalign - compare two multiple alignments SYNOPSIS
compalign [-options] <trusted-alignment> <test-alignment> DESCRIPTION
compalign calculates the fractional "identity" between the trusted alignment and the test alignment. The two files must contain exactly the same sequences, in exactly the same order. The identity of the multiple sequence alignments is defined as the averaged identity over all N(N-1)/2 pairwise alignments. The fractional identity of two sets of pairwise alignments is in turn defined as follows (for aligned known sequences k1 and k2, and aligned test sequences t1 and t2): matched columns / total columns where total columns = the total number of columns in which there is a valid (nongap) symbol in k1 or k2; matched columns = the number of columns in which one of the following is true: k1 and k2 both have valid symbols at a given column; t1 and t2 have the same symbols aligned in a column of the t1/t2 alignment; k1 has a symbol aligned to a gap in k2; that symbol in t1 is also aligned to a gap; k2 has a symbol aligned to a gap in k1; that symbol in t2 is also aligned to a gap. Because scores for all possible pairs are calculated, the algorithm is of order (N^2)L for N sequences of length L; large sequence sets will take a while. OPTIONS
Available options: -h Print short help and usage info. -c Only compare under marked #=CS consensus structure. --informat <s> Specify that both alignments are in format <s> (MSF, for instance). --quiet Suppress verbose header (used in regression testing). SEE ALSO
afetch(1), alistat(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1), weight(1). AUTHOR
Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others). Mon, 01 Aug 2005 15:28:08 -0300 COMPALIGN(1)