compalign(1) [debian man page]
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)
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shuffle(1) Biosquid Manual shuffle(1) NAME
shuffle - randomize the sequences in a sequence file SYNOPSIS
shuffle [options] seqfile DESCRIPTION
shuffle reads a sequence file seqfile, randomizes each sequence, and prints the randomized sequences in FASTA format on standard output. The sequence names are unchanged; this allows you to track down the source of each randomized sequence if necessary. The default is to simply shuffle each input sequence, preserving monosymbol composition exactly. To shuffle each sequence while preserving both its monosymbol and disymbol composition exactly, use the -d option. The -0 and -1 options allow you to generate sequences with the same Markov properties as each input sequence. With -0, for each input sequence, 0th order Markov statistics are collected (e.g. symbol composition), and a new sequence is generated with the same composition. With -1, the generated sequence has the same 1st order Markov properties as the input sequence (e.g. the same disymbol frequencies). Note that the default and -0, or -d and -1, are similar; the shuffling algorithms preserve composition exactly, while the Markov algorithms only expect to generate a sequence of similar composition on average. Other shuffling algorithms are also available, as documented below in the options. OPTIONS
-0 Calculate 0th order Markov frequencies of each input sequence (e.g. residue composition); generate output sequence using the same 0th order Markov frequencies. -1 Calculate 1st order Markov frequencies for each input sequence (e.g. diresidue composition); generate output sequence using the same 1st order Markov frequencies. The first residue of the output sequence is always the same as the first residue of the input sequence. -d Shuffle the input sequence while preserving both monosymbol and disymbol composition exactly. Uses an algorithm published by S.F. Altschul and B.W. Erickson, Mol. Biol. Evol. 2:526-538, 1985. -h Print brief help; includes version number and summary of all options, including expert options. -l Look only at the length of each input sequence; generate an i.i.d. output protein sequence of that length, using monoresidue fre- quencies typical of proteins (taken from Swissprot 35). -n <n> Make <n> different randomizations of each input sequence in seqfile, rather than the default of one. -r Generate the output sequence by reversing the input sequence. (Therefore only one "randomization" per input sequence is possible, so it's not worth using -n if you use reversal.) -t <n> Truncate each input sequence to a fixed length of exactly <n> residues. If the input sequence is shorter than <n> it is discarded (therefore the output file may contain fewer sequences than the input file). If the input sequence is longer than <n> a contiguous subsequence is randomly chosen. -w <n> Regionally shuffle each input sequence in window sizes of <n>, preserving local residue composition in each window. Probably a bet- ter shuffling algorithm for biosequences with nonstationary residue composition (e.g. composition that is varying along the sequence, such as between different isochores in human genome sequence). -B (Babelfish). Autodetect and read a sequence file format other than the default (FASTA). Almost any common sequence file format is recognized (including Genbank, EMBL, SWISS-PROT, PIR, and GCG unaligned sequence formats, and Stockholm, GCG MSF, and Clustal align- ment formats). See the printed documentation for a complete list of supported formats. EXPERT OPTIONS
--informat <s> Specify that the sequence file is in format <s>, rather than the default FASTA format. Common examples include Genbank, EMBL, GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format names. This option overrides the default expected format (FASTA) and the -B Babelfish autodetection option. --nodesc Do not output any sequence description in the output file, only the sequence names. --seed <s> Set the random number seed to <s>. If you want reproducible results, use the same seed each time. By default, shuffle uses a dif- ferent seed each time, so does not generate the same output in subsequent runs with the same input. SEE ALSO
afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), sindex(1), sreformat(1), stranslate(1), weight(1). AUTHOR
Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. 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 Biosquid 1.9g January 2003 shuffle(1)