tmalign(1) [debian man page]
TMALIGN(1) General Commands Manual TMALIGN(1) NAME
TMalign - protein structure alignment SYNOPSIS
TMalign structure.pdbtarget.pdb[options] DESCRIPTION
TMalign performs a structural alignment of proteins. The alignment is scored by the TM-score algorithm. OPTIONS
When started with no options, a summary of commands is given. With two protein structures presented as arguments, the TM-score uses the length of the second protein to be normalised. The final structural alignment is invariant to any of the options below. -L number normalises TM-score by an assigned length (in aa) -a normalises TM-score by the average length of the two structures -b normalises TM-score by the length of the shorter of the two structures -c normalises TM-score by the length of the longer of the two structures -o filename Run TM-align and output the superposition to 'filename.sup' and 'filename.sup_all'. The output files serve as scripts to the program rasmol. To view the superimposed structures of the aligned regions call 'rasmol -script TM.sup' To view the superimposed structures of all regions 'rasmol -script TM.sup_all'. SEE ALSO
http://zhang.bioinformatics.ku.edu/TM-align/, rasmol(1) When using this proram and for more detailed information, please refer to the publication in NucleicAcidsRes. (2005) Volume 33 page 2303ff. by Zhang and Skolnick. AUTHOR
tm-align was written by Zhang and Skolnick. This manual page was written by Steffen Moeller <moeller@debian.org>, for the Debian project (but may be used by others). October 21, 2007 TMALIGN(1)
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CD-HIT-EST(1) User Commands CD-HIT-EST(1) NAME
cdhit-est - run CD-HIT algorithm on RNA/DNA sequences SYNOPSIS
cdhit-est [Options] DESCRIPTION
====== CD-HIT version 4.6 (built on Apr 26 2012) ====== Options -i input filename in fasta format, required -o output filename, required -c sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical amino acids in alignment divided by the full length of the shorter sequence -G use global sequence identity, default 1 if set to 0, then use local sequence identity, calculated as : number of identical amino acids in alignment divided by the length of the alignment NOTE!!! don't use -G 0 unless you use alignment coverage controls see options -aL, -AL, -aS, -AS -b band_width of alignment, default 20 -M memory limit (in MB) for the program, default 800; 0 for unlimitted; -T number of threads, default 1; with 0, all CPUs will be used -n word_length, default 10, see user's guide for choosing it -l length of throw_away_sequences, default 10 -d length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space -s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster -S length difference cutoff in amino acid, default 999999 if set to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60 -aL alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence -AL alignment coverage control for the longer sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues -aS alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence -AS alignment coverage control for the shorter sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues -A minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this value for both sequences -uL maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing gaps) must not be more than 10% of the sequence -uS maximum unmatched percentage for the shorter sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tail- ing gaps) must not be more than 10% of the sequence -U maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more than 10 bases -B 1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on hard drive it is recommended to use -B 1 for huge databases -p 1 or 0, default 0 if set to 1, print alignment overlap in .clstr file -g 1 or 0, default 0 by cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast clus- ter). If set to 1, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode) but either 1 or 0 won't change the representatives of final clusters -r 1 or 0, default 1, by default do both +/+ & +/- alignments if set to 0, only +/+ strand alignment -mask masking letters (e.g. -mask NX, to mask out both 'N' and 'X') -match matching score, default 2 (1 for T-U and N-N) -mismatch mismatching score, default -2 -gap gap opening score, default -6 -gap-ext gap extension score, default -1 -bak write backup cluster file (1 or 0, default 0) -h print this help Questions, bugs, contact Limin Fu at l2fu@ucsd.edu, or Weizhong Li at liwz@sdsc.edu For updated versions and information, please visit: http://cd-hit.org cd-hit web server is also available from http://cd-hit.org If you find cd-hit useful, please kindly cite: "Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong Li, Lukasz Jaroszewski & Adam Godzik. Bioinformatics, (2001) 17:282-283 "Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences", Weizhong Li & Adam Godzik. Bioinformatics, (2006) 22:1658-1659 cd-hit-est 4.6-2012-04-25 April 2012 CD-HIT-EST(1)