10-02-2010
Hex numbering sequence
Friends, I am looking for a small script which generates HEX sequence. Input to the script is starting hex number - Group ID and number of members a group should have and total groups.
e.g: Here we are generating 2 groups with 4 Members each starting with hex 036A.
Output:
Group ID 036A, members below;
members 036B:036D;
Group ID 036E, members below;
members 036F:0371;
Help is heartily appreciated
---------- Post updated at 06:54 AM ---------- Previous update was at 06:51 AM ----------
Output in following format will also do:
Group ID 036A, members below;
member 036B
member 036C
member 036D
Group ID 036E, members below;
member 036F
member 0370
member 0371
Please help...
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LEARN ABOUT DEBIAN
theseus_align
THESEUS_ALIGN(1) General Commands Manual THESEUS_ALIGN(1)
NAME
theseus_align - quick-and-dirty way to superimpose proteins
SYNOPSIS
theseus_align [theseus options] -f pdbfile1.pdb pdbfile2.pdb ...
OPTIONS
The options given to the script will be passed on to theseus. For a complete description, see the man page for theseus (1).
DESCRIPTION
This manual page briefly documents briefly the script theseus_align, designed for a quick-and-dirty way to ML superposition proteins with
different sequences. It should work very well when the protein sequences are relatively similar, although the ML method will still give
much better results than least-squares when the sequences are moderately divergent. Technically, this procedure gives a structure-based
superposition of a sequence-based alignment. It does not perform a structure-based alignment.
First, the script uses theseus to create FASTA formatted sequence files corresponding to the exact protein sequences found in the pdb files
that you supply.
Second, these sequences are aligned using the multiple sequence alignment program of your choice. The script can easily be modified for
CLUSTALW, T_COFFEE, KALIGN, DIALIGN2, or MAFFT. Any multiple sequence alignment program can be used, as long as it can generate clustal-
formatted files. However, I highly recommend Bob Edgar's MUSCLE program for both its speed and accuracy. (For more info see
http://www.drive5.com/muscle/ .)
Third, theseus performs a superposition of the structures using the sequence alignment as a guide.
The installed version of theseus_align uses muscle (1) for doing the multiple sequence alignment. If you wish to use one of the other pro-
grams mentioned above, you'll have to copy the script to your own directory and edit it.
SEE ALSO
theseus (1), muscle (1), clustalw (1), t_coffee (1), kalign (1), dialign2 (1), mafft (1). All of these programs can be installed on Debian
or Ubuntu systems using apt-get (8).
AUTHOR
theseus_align was written by Douglas L. Theobald, Department of Biochemistry, Brandeis University.
November, 2008 THESEUS_ALIGN(1)