09-01-2011
Radulov
That's great! The only part that is missing is the headers (>Sequence ID) for each sequence. How can I modify your perl script so it can include the headers for each and every sequence?
Thanks!
9 More Discussions You Might Find Interesting
1. Windows & DOS: Issues & Discussions
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)
Discussion started by: saabir
1 Replies
2. Shell Programming and Scripting
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)
Discussion started by: bestbuyernc
2 Replies
3. Shell Programming and Scripting
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)
Discussion started by: madhusmita
9 Replies
4. Shell Programming and Scripting
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)
Discussion started by: MissI
3 Replies
5. Shell Programming and Scripting
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)
Discussion started by: akreibich07
5 Replies
6. Solaris
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)
Discussion started by: kl0x
4 Replies
7. HP-UX
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)
Discussion started by: mohtashims
1 Replies
8. Shell Programming and Scripting
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)
Discussion started by: margarita
5 Replies
9. Shell Programming and Scripting
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
lastal
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)