alistat(1) [debian man page]
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)
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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)