probalign(1) [debian man page]
PROBALIGN(1) User Commands PROBALIGN(1) NAME
probalign - Align sequences in MFAFILE(s) and print result to standard output DESCRIPTION
PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the standard output. Written by Satish Chikkagoudar and Usman Roshan using code from PROBCONS version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). PROBALIGN 1.4 comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. See the README file for details. Usage: probalign [OPTION]... [MFAFILE]... Description: Align sequences in MFAFILE(s) and print result to standard output -clustalw use CLUSTALW output format instead of MFA -v, --verbose report progress while aligning (default: off) -a, --alignment-order print sequences in alignment order rather than input order (default: off) -T, -temperature Sets the thermodynamic temperature parameter (default: 5 (for protein data mode), 1 ( for nucleotide data mode)). -score_matrix, --score_matrix Sets the type of scoring matrix used to calculate the posterior probabilities (default: gonnet_160, representing gonnet 160, refer README for details) -go, --gap-open This option can be used to specify the gap open parameter. The default for Gonnet 160 (protein) is 22 and nucleotide (simple matrix) is 4. -ge, --gap-extension This option can be used to specify the gap extension parameter. The default for Gonnet 160 (protein) is 1 and nucleotide (simple matrix) is 0.25. -nuc Specify this option to indicate that inputted sequences are nucleotide sequences -prot Specify this option to indicate that inputted sequences are protein sequences [DEFAULT] -showPP Outputs the posterior probabilities of alignment columns as a new sequence named Posterior Probabilities (The probability values are scaled to be between integers between 0 and 9). probalign 1.4 May 2011 PROBALIGN(1)
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SSEMATCH(1e) EMBOSS Manual for Debian SSEMATCH(1e) NAME
ssematch - Search a DCF file for secondary structure matches. SYNOPSIS
ssematch -ssinfile infile -dcfinfile infile [-datafile matrixf] -maxhits integer [-rgapopen float] [-rgapextend float] [-egapopen float] [-egapextend float] -outssfile outfile -outsefile outfile -logfile outfile ssematch -help DESCRIPTION
ssematch is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Utils:Database creation" command group(s). OPTIONS
Input section -ssinfile infile This option specifies the name of the file of secondary structure (input). -dcfinfile infile This option specifies the name of the DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. -datafile matrixf This option specifies the secondary structure substitution matrix. Default value: SSSUB Required section -maxhits integer This option specifies the number of top-scoring matches to report. Default value: 5 Additional section -rgapopen float This options specifies the gap insertion penalty for reside-based alignment. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: 10 -rgapextend float This options specifies the gap extension penalty for residue-based alignment. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. Default value: 0.5 -egapopen float This options specifies the gap insertion penalty for element-based alignment. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: 10 -egapextend float This options specifies the gap extension penalty for secondary structure element-based alignment. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. Default value: 0.5 Output section -outssfile outfile This option specifies the name of the file containing top-scoring domains for residue-based alignment (output).A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). -outsefile outfile This option specifies the name of the file containing top-scoring domains for secondary structure element-based alignment (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). -logfile outfile This option specifies the name of the ssematch log file (output). Default value: ssematch.log BUGS
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). SEE ALSO
ssematch is fully documented via the tfm(1) system. AUTHOR
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Wrote the script used to autogenerate this manual page. COPYRIGHT
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. DOMAINATRIX 0.1.0+20100721 08/11/2010 SSEMATCH(1e)