NAME
	revtrans - performs a reverse translation of a peptide alignment

SYNOPSIS
	revtrans dnafile pepfile [-v] [-h] [-gapin chars] [-gapout char]
	 [-Idna format] [-Ipep format] [-mtx tablename/file] [-match method]
	 [-O format] [outfile]

DESCRIPTION
       Reads a set of aligned peptide sequences from pepfile and uses
       the corresponding DNA sequences from dnafile to construct a
       reverse translated version of the alignment.

       By default the input file formats are auto detected and the
       corresponding DNA and peptide sequences is found by translation.

       In the typical case this means that the user only need to
       supply the DNA and peptide sequences, and may safely ignore
       the more advanced options. E.g :

	       revtrans kinases.dna.fsa kinases.prot.aln

       The final alignment is written to STDOUT or outfile if specified,
       and is by default in FASTA format.

OPTIONS
	-h
		Help. Print this help information.

	-gapin chars
		Specify gap characters in the input sequences.
		Default is '.-~'

	-gapout	char
		Specify which character should be used for gaps in the
		output.
		Default is '-'

	-Idna format
		Specify format of the input DNA file.
		Valid formats are: auto (default), fasta, msf and aln

	-Ipep format
		Specify format of the input peptide file.
		Valid formats are: auto (default), fasta, msf and aln

	-O format
		Specify format of the output file.
		Valid formats are: fasta (default), msf and aln

	-mtx tablename/file
		Use alternative translation matrix instead of the build-in
		Standard Genetic Code for translation.

		If "tablename" is 1-6,9-16 or 21-23 one of the alternative
		translation tables defined by the NCBI taxonomy group will be
		used.

		Briefly, the following tables are defined:
		-----------------------------------------
		 1: The Standard Code
		 2: The Vertebrate Mitochondrial Code
		 3: The Yeast Mitochondrial Code
		 4: The Mold, Protozoan, and Coelenterate Mitochondrial Code
		    and the Mycoplasma/Spiroplasma Code
		 5: The Invertebrate Mitochondrial Code
		 6: The Ciliate, Dasycladacean and Hexamita Nuclear Code
		 9: The Echinoderm and Flatworm Mitochondrial Code
		10: The Euplotid Nuclear Code
		11: The Bacterial and Plant Plastid Code
		12: The Alternative Yeast Nuclear Code
		13: The Ascidian Mitochondrial Code
		14: The Alternative Flatworm Mitochondrial Code
		15: Blepharisma Nuclear Code
		16: Chlorophycean Mitochondrial Code
		21: Trematode Mitochondrial Code
		22: Scenedesmus obliquus mitochondrial Code
		23: Thraustochytrium Mitochondrial Code

		See http://www.ncbi.nlm.nih.gov/Taxonomy [Genetic Codes]
		for a detailed description. Please notice that the table
		of start codons is also used (see the -allinternal option
		below for details).

		If a filename is supplied the translation table is read from
		file instead.

		The file should contain one line per codon in the format:

		codon<whitespace>aa-single letter code

		All 64 codons must be included. Stop codons is specified
		by "*". T and U is interchangeable. Blank lines and lines
		starting with "#" are ignored.

		See the "gcMitVertebrate.mtx" file in the RevTrans source
		distribution for a well documented example.

	-allinternal
		By default the very first codon in each sequences is assumed
		to be the initial codon on the transcript. This means certain
		non-methionine codons actually codes for metionine at this
		position. For example "TTG" in the standard genetic code (see
		above).

		Selecting this option treats all codons as internal codons.

	-readthroughstop
		Allow the translation to continue after a stop codon is reached.
		The stop codon will be marked as "*".

		Be careful that stop codons have been addressed in the same manner
		in the input peptide alignment.

	-match method
		Specify how to match the corresponding DNA and peptide
		sequences. Valid methods are: trans (default), name and pos.

		Please note that both DNA and peptide sequence should have
		unique names, regardless of the matching method.

		trans:
			Match sequences by translation. The DNA sequences are
			translated using the standard genetic code (default)
			or an alternative translation matrix if the -mtx
			option is used.

		name:
			Match sequences by name. Please note that for FASTA
			files everything after the ">" is considered the
			sequence name.

		pos:
			Match by position. The sequence are matched by position
			in the files (first DNA sequence with first peptide
			sequence etc.).
	-v
		Verbose. Print extra information about files, sequences
		and the progress in general to STDERR.

		The verbose level can be set to three degrees of
		detail.

		-v:   verbose level 1
			Info about files, number of sequences read etc.
			Use this as the first try if something needs
			investigation.

		-vv:  verbose level 2
			As level 1 +
			Print detailed info about all the sequence names.

		-vvv: verbose level 3
			As level 2 +
			Do a sanity check on the degapped length of the
			sequences. Warn if the sizes do not match.

AUTHOR
	Rasmus Wernersson, raz@cbs.dtu.dk
	September 2002, February 2003, July 2004, April 2005

FILES
	revtrans.py, mod_translate.py, mod_seqfiles.py,
	ncbi_genetic_codes.py

WEB PAGE
	http://www.cbs.dtu.dk/services/RevTrans/

REFERENCE
	Rasmus Wernersson and Anders Gorm Pedersen.
	RevTrans - Constructing alignments of coding DNA from aligned amino
	acid sequences.
	Nucl. Acids Res., 2003, 31(13), 3537-3539.
