Here's my problem:
I have a laptop running Windows XP Pro with no internal CD or Floppy drives. I want to install Linux on it. I don't care about the Windows XP Pro installation, in fact I would like to install Linux over the entirety of the HD. However I cannot boot from any external CD drive... (1 Reply)
Hello. I am trying to convert occurrences of 'NULL' from a datafile. The 'NULL' occurences appears at this:
|NULL| NULL|NULL| NULL|NULL| NULL|NULL| NULL|
There should be 52 fields per line.
I would like any occurrence of | NULL| or |NULL| to appear as '||'
Currently I am using this sed... (2 Replies)
I have a file contains
TASK gsnmpproxy {
CommandLine = $SMCHOME/bin/gsnmpProxy.exe
}
TASK gsnmpdbgui {
CommandLine = $SMCHOME/bin/gsnmpdbgui.exe
I would like to comment and than uncomment specific task eg TASK gsnmpproxy
Pls suggest how to do in shell script (9 Replies)
I have an task definition listing xml file that contains a list of tasks such as
<TASKLIST
<TASK definition="Completion date" id="Taskname1" Some other
<CODE name="Code12"
<Parameter pname="Dog" input="5.6" units="feet" etc /Parameter>
<Parameter... (3 Replies)
Hi all,
Using Perl, I need to extract DNA bases from a GenBank file for a given plant species. A sample GenBank file is here...
Nucleotide
This is saved on my computer as NC_001666.gb. I also have a file that is saved on my computer as NC_001666.txt. This text file has a list of all... (5 Replies)
Hi folks!
My first post here.
I'm working on a script that retrieves a range of files from a list depending on a range of time.
UPDATE:
I've seen it could be difficult to read all this thing, so I'll make a summarize it..
How come I do this and take a result..
grep "..\:.." lista.new |... (4 Replies)
Hi,
I have a multihomed system HP-UX with two NIC cards having IP address 10.9.0.13 & 10.9.0.45
I have two weblogic servers running one listening on "10.9.0.13" and the other on "10.9.0.45"
Given a PID how is it possible to extract the IP Address that the weblogic server is using and... (1 Reply)
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
I am trying to write a bash script that would be able to read DNA sequences (each line in the file is a sequence) from a file, where sequences are separated by an empty line. I am then to find the amino acid that these DNA sequences encode per codon (each group of three literals.) For example, if I... (3 Replies)
Discussion started by: faizlo
3 Replies
LEARN ABOUT DEBIAN
blastclust
BLASTCLUST(1) NCBI Tools User's Manual BLASTCLUST(1)NAME
blastclust - BLAST score-based single-linkage clustering
SYNOPSIS
blastclust [-] [-C] [-L X] [-S X] [-W N] [-a N] [-b F] [-c filename] [-d filename] [-e F] [-i filename] [-l filename] [-o filename] [-p F]
[-r filename] [-s filename] [-v [filename]]
DESCRIPTION
blastclust automatically and systematically clusters protein or DNA sequences based on pairwise matches found using the BLAST algorithm in
case of proteins or Mega BLAST algorithm for DNA. In the latter case a single Mega BLAST search is performed for all the sequences combined
against a database created from the same sequences. blastclust finds pairs of sequences that have statistically significant matches and
clusters them using single-linkage clustering.
OPTIONS
A summary of options is included below.
- Print usage message
-C Complete unfinished clustering
-L X Length coverage threshold (default = 0.9)
-S X Score coverage threshold (bit score / length if < 3.0, percentage of identities otherwise; default = 1.75)
-W N Use words of size N (length of best perfect match; zero invokes default behavior: 3 for proteins, 32 for nucleotides)
-a N Number of CPU's to use (default = 1)
-b F Do not require coverage on both neighbours
-c filename
Read advanced options from configuration file filename
-d filename
Input as a database
-e F Disable id parsing in database formatting
-i filename
FASTA input file (program will format the database and remove files in the end; default = stdin)
-l filename
Restrict reclustering to id list in filename
-o filename
Output file for list of clusters (default = stdout)
-p F Input is nucleotides, not proteins.
-r filename
Restore neighbors for reclustering from filename
-s filename
Save all neighbours to filename
-v [filename]
Print verbose progress messages (to filename)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO blast(1), formatdb(1), /usr/share/doc/blast2/blastclust.html, <http://www.ncbi.nlm.nih.gov/BLAST/>
NCBI 2004-06-25 BLASTCLUST(1)