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)
Check Out this Related Man Page
LASTAL(1) User Commands LASTAL(1)NAME
lastal - genome-scale comparison of biological sequences
SYNOPSIS
lastal [options] lastdb-name fasta-sequence-file(s)
DESCRIPTION
Find local sequence alignments.
Score options (default settings): -r: match score (DNA: 1, protein: blosum62, 0<Q<5: 6) -q: mismatch cost (DNA: 1, protein: blosum62,
0<Q<5: 18) -p: file for residue pair scores -a: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21) -b: gap extension cost (DNA: 1, pro-
tein: 2, 0<Q<5: 9) -c: unaligned residue pair cost (100000) -F: frameshift cost (off) -x: maximum score drop for gapped alignments
(max[y, a+b*20]) -y: maximum score drop for gapless alignments (t*10) -z: maximum score drop for final gapped alignments (x) -d: minimum
score for gapless alignments (e*3/5) -e: minimum score for gapped alignments (DNA: 40, protein: 100, 0<Q<5: 180)
Cosmetic options (default settings): -h: show all options and their default settings -v: be verbose: write messages about what lastal is
doing -o: output file -f: output format: 0=tabular, 1=maf (1)
Miscellaneous options (default settings): -s: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) -m: maximum multiplicity for
initial matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query position (infinity) -k:
step-size along the query sequence (1) -i: query batch size (1 MiB if Q>0, else 16 MiB if j=0, else 128 MiB) -u: mask lowercase during
extensions: 0=never, 1=gapless,
2=gapless+gapped but not final, 3=always (2 if lastdb -c and Q<5, else 0)
-w: supress repeats inside exact matches, offset by this distance or less (1000) -G: genetic code file -t: 'temperature' for calculating
probabilities (1/lambda) -g: 'gamma' parameter for gamma-centroid and LAMA (1) -j: output type: 0=match counts, 1=gapless, 2=redundant
gapped, 3=gapped,
4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA (3)
-Q: input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina,
4=prb, 5=PSSM (0)
REPORTING BUGS
Report bugs to: last (ATmark) cbrc (dot) jp
LAST home page: http://last.cbrc.jp/
lastal 199 May 2012 LASTAL(1)