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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alistat(1) Biosquid Manual alistat(1) NAME
alistat - show statistics for a multiple alignment file SYNOPSIS
alistat [options] alignfile DESCRIPTION
alistat reads a multiple sequence alignment from the file alignfile in any supported format (including SELEX, GCG MSF, and CLUSTAL), and shows a number of simple statistics about it. These statistics include the name of the format, the number of sequences, the total number of residues, the average and range of the sequence lengths, the alignment length (e.g. including gap characters). Also shown are some percent identities. A percent pairwise alignment identity is defined as (idents / MIN(len1, len2)) where idents is the number of exact identities and len1, len2 are the unaligned lengths of the two sequences. The "average percent identity", "most related pair", and "most unrelated pair" of the alignment are the average, maximum, and minimum of all (N)(N-1)/2 pairs, respectively. The "most distant seq" is calculated by finding the maximum pairwise identity (best relative) for all N sequences, then finding the minimum of these N numbers (hence, the most outlying sequence). OPTIONS
-a Show additional verbose information: a table with one line per sequence showing name, length, and its highest and lowest pairwise identity. These lines are prefixed with a * character to enable easily grep'ing them out and sorting them. For example, alistat -a foo.slx | grep * | sort -n +3 gives a ranked list of the most distant sequences in the alignment. Incompatible with the -f option. -f Fast; use a sampling method to estimate the average %id. When this option is chosen, alistat doesn't show the other three pairwise identity numbers. This option is useful for very large alignments, for which the full (N)(N-1) calculation of all pairs would be prohibitive (e.g. Pfam's GP120 alignment, with over 10,000 sequences). Incompatible with the -a option. -h Print brief help; includes version number and summary of all options, including expert options. -q be quiet - suppress the verbose header (program name, release number and date, the parameters and options in effect). -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 format (FASTA) and the -B Babelfish autodetection option. SEE ALSO
afetch(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(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 alistat(1)