Hello,
Attached is my very simple C++ code to remove any substrings (DNA sequence) of each other, i.e. any redundant sequence is removed to get unique sequences. Similar to sort | uniq command except there is reverse-complementary for DNA sequence. The program runs well with small dataset, but when I increase the data size to ~1,000 entries (some maybe 100,000bp long), it took about 2 hours to finish.
My question is: How to improve the performance of my code?
It seems memory issue can be excluded as 256GB RAM is available.
1) What are the room for coding techniques based on my current algorithms, which is a simple "sorting---looping---comparing" with complexity n^2 ?
2) What are the better algorithms, for sure there are many?
Either of the two questions is too complicate for myself, but I am wondering if anybody can give me some help to increase the performance of the program. Thanks a lot!
Hi ,
i'm searching for files over many Aix servers with rsh command using this request :
find /dir1 -name '*.' -exec ls {} \;
and then count them with "wc"
but i would improve this search because it's too long and replace directly find with ls command but "ls *. " doesn't work.
and... (3 Replies)
Hi All,
I am using grep command to find string "abc" in one file .
content of file is
***********
abc = xyz
def= lmn
************
i have given the below mentioned command to redirect the output to tmp file
grep abc file | sort -u | awk '{print #3}' > out_file
Then i am searching... (2 Replies)
hi someone tell me which ways i can improve disk I/O and system process performance.kindly refer some commands so i can do it on my test machine.thanks, Mazhar (2 Replies)
I have a data file of 2 gig
I need to do all these, but its taking hours, any where i can improve performance, thanks a lot
#!/usr/bin/ksh
echo TIMESTAMP="$(date +'_%y-%m-%d.%H-%M-%S')"
function showHelp {
cat << EOF >&2
syntax extreme.sh FILENAME
Specify filename to parse
EOF... (3 Replies)
Hi Friends,
I wrote the below shell script to generate a report on alert messages recieved on a day. But i for processing around 4500 lines (alerts) the script is taking aorund 30 minutes to process.
Please help me to make it faster and improve the performace of the script. i would be very... (10 Replies)
Hi All,
I have written a script as follows which is taking lot of time in executing/searching only 3500 records taken as input from one file in log file of 12 GB Approximately.
Working of script is read the csv file as an input having 2 arguments which are transaction_id,mobile_number and search... (6 Replies)
Hi,
I have around one lakh records. I have used XML for the creation of the data.
I have used these 2 Perl modules.
use XML::DOM;
use XML::LibXML;
The data will loo like this and most it is textual entries.
<eid>19000</eid>
<einfo>This is the ..........</einfo>
......... (3 Replies)
Hi ,
i wrote a script to convert dates to the formate i want .it works fine but the conversion is tkaing lot of time . Can some one help me tweek this script
#!/bin/bash
file=$1
ofile=$2
cp $file $ofile
mydates=$(grep -Po '+/+/+' $ofile) # gets 8/1/13
mydates=$(echo "$mydates" | sort |... (5 Replies)
Discussion started by: vikatakavi
5 Replies
LEARN ABOUT DEBIAN
vecscreen
VECSCREEN(1) NCBI Tools User's Manual VECSCREEN(1)NAME
vecscreen - find nucleic acid segments of possible vector origin
SYNOPSIS
vecscreen [-] [-d str] [-f N] [-i filename] [-o filename]
DESCRIPTION
vecscreen is a system for quickly identifying segments of a nucleic acid sequence that may be of vector origin. NCBI developed vecscreen to
minimize the incidence and impact of vector contamination in public sequence databases. GenBank Annotation Staff use vecscreen to verify
that sequences submitted for inclusion in the database are free from contaminating vector sequence. Any sequence can be screened for vector
contamination using vecscreen.
vecscreen searches a query for segments that match any sequence in a specialized non-redundant vector database (UniVec). The search uses
BLAST with parameters preset for optimal detection of vector contamination. Those segments of the query that match vector sequences are
categorized according to the strength of the match, and their locations are displayed (see example positive result).
vecscreen is designed to quickly check a nucleic acid sequence for the presence of vector contamination and to show which segments within
the sequence may be of vector origin. Although a vecscreen search against UniVec will not identify the vector that is the most likely
source of the contamination, this can usually be deduced from the cloning history of the sequenced DNA.
OPTIONS
A summary of options is included below.
- Print usage message
-d str Database (default = UniVec)
-f N Output format:
0 HTML format, with alignments (default)
1 HTML format, no alignments
2 Text list, with alignments
3 Text list, no alignments
-i filename
Query File (default = stdin)
-o filename
VecScreen report Output File (default = stdout)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO
<http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen_docs.html>
NCBI 2001-10-05 VECSCREEN(1)