ncoils(1) [debian man page]
NCOILS(1) User Commands NCOILS(1) NAME
ncoils - prediction of coiled-coil secondary structure elements SYNOPSIS
ncoils [OPTION] < [FASTA FILE] ncoils -f < /usr/share/doc/ncoils/1srya.fa DESCRIPTION
ncoils is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. OPTIONS
-f, -fasta fasta output - coils as 'x', like '-x' in seg -c concise mode - which sequences have any coils (and how many) -min_seg <int> for concise mode - only report sequence if >= min coil segments -min_P <float> minimum P to define coil segment; DEFAULT = 0.5 -win <int> window size; DEFAULT = 21 -w weight heptad positions a&d the same as b,c,e,f,g -v verbose/debug mode - print extra junk EXAMPLES
"coils-wrap -m MTIDK -i /usr/share/doc/ncoils/1srya.fa -o /tmp/coils.out -r /tmp/coils_raw.txt && less /tmp/coils.out /tmp/coils_raw.txt" "ncoils -win 14 < /usr/share/doc/ncoils/1srya.fa" ENVIRONMENT
COILSDIR - specifies the directory containing the file new.mat overriding the default /usr/share/ncoils FILES
/usr/share/ncoils/*.mat matrix data files AUTHOR
R.B. Russell, A.N. Lupas COPYRIGHT AND LICENSE
GPL Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164 SEE ALSO
coils-wrap(1), "usr/share/doc/coils/README", http://www.russelllab.org/cgi-bin/coils/coils-svr.pl <http://www.russelllab.org/cgi- bin/coils/coils-svr.pl> A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996 A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991 2002 2011-10-29 NCOILS(1)
Check Out this Related Man Page
GLAM2-PURGE(1) glam2 Manual GLAM2-PURGE(1) NAME
glam2-purge - Removes redundant sequences from a FASTA file SYNOPSIS
glam2-purge file score [options] DESCRIPTION
glam2-purge is a modified version of Andrew Neuwald's purge program that removes redundant sequences from a FASTA file. This is recommended in order to prevent highly similar sequences distorting the search for motifs. Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user. The output file is named <file>.<score>. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/-1 scoring scheme for DNA. Purge can also be used to mask tandem repeats. It uses the XNU program for this purpose. OPTIONS
-n Sequences are DNA (default: protein). -b Use blast heuristic method (default for protein). -e Use an exhaustive method (default for DNA). -q Keep first sequence in the set. -x Use xnu to mask protein tandem repeats. SEE ALSO
glam2(1), glam2format(1), glam2mask(1), glam2scan(1), xnu(1) The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/. REFERENCES
Purge was written by Andy Neuwald and is described in more detail in Neuwald et al., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618-1632, 1995. Please cite it if you use Purge. If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press). AUTHORS
Andrew Neuwald Author of purge, renamed glam2-purge in Debian. Martin Frith Modified purge to be ANSI standard C and improved the user interface. Timothy Bailey Modified purge to be ANSI standard C and improved the user interface. Charles Plessy <plessy@debian.org> Formatted this manpage in DocBook XML for the Debian distribution. COPYRIGHT
The source code and the documentation of Purge and GLAM2 are released in the public domain. GLAM2 1056 05/19/2008 GLAM2-PURGE(1)