theseus_align(1) [debian man page]

THESEUS_ALIGN(1)					      General Commands Manual						  THESEUS_ALIGN(1)

NAME

       theseus_align - quick-and-dirty way to superimpose proteins

SYNOPSIS

       theseus_align [theseus options] -f pdbfile1.pdb pdbfile2.pdb ...

OPTIONS

       The options given to the script will be passed on to theseus. For a complete description, see the man page for theseus (1).

DESCRIPTION

       This  manual  page briefly documents briefly the script theseus_align, designed for a quick-and-dirty way to ML superposition proteins with
       different sequences. It should work very well when the protein sequences are relatively similar, although the ML  method  will  still  give
       much  better  results  than least-squares when the sequences are moderately divergent.  Technically, this procedure gives a structure-based
       superposition of a sequence-based alignment. It does not perform a structure-based alignment.

       First, the script uses theseus to create FASTA formatted sequence files corresponding to the exact protein sequences found in the pdb files
       that you supply.

       Second,	these  sequences  are  aligned using the multiple sequence alignment program of your choice. The script can easily be modified for
       CLUSTALW, T_COFFEE, KALIGN, DIALIGN2, or MAFFT. Any multiple sequence alignment program can be used, as long as it  can	generate  clustal-
       formatted  files.  However,  I  highly  recommend  Bob  Edgar's	MUSCLE	program  for  both  its  speed	and  accuracy.	(For more info see
       http://www.drive5.com/muscle/ .)

       Third, theseus performs a superposition of the structures using the sequence alignment as a guide.

       The installed version of theseus_align uses muscle (1) for doing the multiple sequence alignment. If you wish to use one of the other  pro-
       grams mentioned above, you'll have to copy the script to your own directory and edit it.

SEE ALSO

       theseus (1), muscle (1), clustalw (1), t_coffee (1), kalign (1), dialign2 (1), mafft (1).  All of these programs can be installed on Debian
       or Ubuntu systems using apt-get (8).

AUTHOR

       theseus_align was written by Douglas L. Theobald, Department of Biochemistry, Brandeis University.

								  November, 2008						  THESEUS_ALIGN(1)

KALIGN(1)							Kalign User Manual							 KALIGN(1)

NAME

       kalign - performs multiple alignment of biological sequences.

SYNOPSIS

       kalign [infile.fasta] [outfile.fasta] [Options]

       kalign [-i infile.fasta] [-o outfile.fasta] [Options]

       kalign [< infile.fasta] [> outfile.fasta] [Options]

DESCRIPTION

       Kalign is a command line tool to perform multiple alignment of biological sequences. It employs the Muth?Manber string-matching algorithm,
       to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an
       approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global
       alignment.

OPTIONS

       -s -gpo -gapopen -gap_open x
	   Gap open penalty .

       -e -gpe -gap_ext -gapextension x
	   Gap extension penalty.

       -t -tgpe -terminal_gap_extension_penalty x
	   Terminal gap penalties.

       -m -bonus -matrix_bonus x
	   A constant added to the substitution matrix.

       -c -sort <input, tree, gaps.>
	   The order in which the sequences appear in the output alignment.

       -g -feature
	   Selects feature mode and specifies which features are to be used: e.g. all, maxplp, STRUCT, PFAM-A?

       -same_feature_score
	   Score for aligning same features.

       -diff_feature_score
	   Penalty for aligning different features.

       -d -distance <wu, pair>
	   Distance method

       -b -tree -guide-tree <nj, upgma>
	   Guide tree method.

       -z -zcutoff
	   Parameter used in the wu-manber based distance calculation.

       -i -in -input
	   Name of the input file.

       -o -out -output
	   Name of the output file.

       -a -gap_inc
	   Increases gap penalties depending on the number of existing gaps.

       -f -format <fasta, msf, aln, clu, macsim>
	   The output format.

       -q -quiet
	   Print nothing to STDERR. Read nothing from STDIN.

REFERENCES

       o   Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics
	   6:298

       o   Timo Lassmann, Oliver Frings and Erik L. L. Sonnhammer (2009) Kalign2: high-performance multiple alignment of protein and nucleotide
	   sequences allowing external features. Nucleic Acid Research 3:858?865.

AUTHORS

       Timo Lassmann <timolassmann@gmail.com>
	   Upstream author of Kalign.

       Charles Plessy <plessy@debian.org>
	   Wrote the manpage.

COPYRIGHT

       Copyright (C) 2004, 2005, 2006, 2007, 2008 Timo Lassmann

       Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the
       Free Software Foundation.

       This manual page was written by Charles Plessy <plessy@debian.org> for the Debian(TM) system (but may be used by others). Permission is
       granted to copy, distribute and/or modify this document under the same terms as kalign itself.

       On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common-licenses/GPL-2.

kalign 2.04							 February 25, 2009							 KALIGN(1)