BOL: All site questions

Bioinformatics tools used in bacterial plant pathogen studies...

Mahesh Lawate — Mon, 19 Aug 2013 02:58:28 -0500

I would like to know different bioinformatics tools and softwares used in plant pathogenic bacterial research studies(particlularly Xanthomonas group). My specific interest lies Xanthomonas axonopodis pv. punicae pathogen of bacterial blight of pomegranate. I want to study this bacterium independently till I apply to a research laboratory in future. I have basic knowledge of bioinformatics. Please help me.

Thank You.

Is it possible to find out particular secondary metabolite from sequenced genome? or even from the in silico metabolic models of that living organisms?

Swapnil Bhalke — Fri, 16 Aug 2013 02:09:59 -0500

Hello everyone,

I am basically biotechnology student.I am just aware about very basic knowledge about bioinformatics and programming language.The genome for Yarrowia lipolytica is already sequenced and recently two in silico metabolic models also developed.Please help me to find out enzyme cascade reqired for production of volatile compounds after fatty acid degradation and what other commecial products can be obtained from this enzyme cascade.

What type of work available in Bioinformatics?

Madhvan Reddy — Tue, 13 Aug 2013 13:07:55 -0500

Hi All,

I am new to bioinformatics, recently dived into it. I would like to know which type of works, bioinformatics knowledge gonna offer me in near future.

In sequence read archive(SRA) database, is there any option to fill the MD5 checksum box. What i have to write there??

minakshi — Tue, 13 Aug 2013 05:17:04 -0500

What is MD5 checksum?

minakshi — Tue, 13 Aug 2013 03:48:55 -0500

Is bioinformatics industry has potential and future scope?

Manshi Raghubanshi — Sat, 10 Aug 2013 21:55:21 -0500

I am new to bioinformatics and bit confused regarding future. It looks to me that bioinformatics sector have limited opportunity. Need your suggestions and comments.

How to separate FASTA sequences by their name in files?

Manshi Raghubanshi — Fri, 09 Aug 2013 11:16:45 -0500

I have one big file with lots of fasta sequences. I would like to separate the sequences by their name in files. Can anyone please help me to do so. Thanks for your time.

Sample fasta sequences in file:

>SBI_03055_PP_HisKa|Streptomyces bingchenggensis BCW-1
MSSSDAARTGSAEGARDSKRVRTRRTLRDWIVDVCCISLAALFSLTASESMATDPSVSDE
ALFADLMAGVVACLALWLRRRRPVELALVLLAAGVVSYYVAGPLLVALFTVAVHRPLRTV
AWVGGAALAQIFAAPAVHPDPDLDYIGDVLLGALLVSGAIGWGMFVRSRRLLLESLRERA
ARAEAEAALRAERTQRLTRERIAREMHDVLAHRLSLLSVHAGALEYRADASPQEVAEAAG
VIRSSAHQALQDLREVIGVLRAPDSDATAEGSPPDRPQPTLADLPRLVEESRRAGMRVTL
SDEAGVAGADA
>SBI_03056_RR_NarL|Streptomyces bingchenggensis BCW-1
VSSSPPESTDPAPAPTPTPPAPDPAPTPTPGSGPSLTPIRLLVVDDDPLVRAGLRLMLGG
ASSGIEIVGEASDGAEVAALVDRHSPDVVLMDIRMPTVDGLTATEQLRQREPAPEVVVLT
TFNADEHVLRALRAGAAGFVLKDTPPADLVAAVRRVAAGEPVLSPTVTQQLIEHVAGSGR
DARQERARALLDQLNDREREVAVAVGEGKSNAEISAGLFMSVATVKTHVSRILTKLDLNN
RVQIALLAHDAGLLE

How to find a files in a folder or sub folders?

Manshi Raghubanshi — Thu, 08 Aug 2013 13:26:30 -0500

Hi Bioinformaticians,

I am new to bioinformatics and Perl. So, please execuse me if I disturb you all with newbie question.

I am strugling to find a specific files (cattle_genome.fasta) from a folder and sub folders, and read it. I got some of the help form this website http://stackoverflow.com/questions/5651659/read-all-files-in-a-directory-in-perl in which they explain the extraction method using opendir function. It is suitable only when we have know directory name and depth of the folder.

Can you please suggest me any other method to find the file recursively and read or write the specific fasta file.

How to find Operating System name using perl script?

Neel — Tue, 06 Aug 2013 17:37:47 -0500

Hi All,
Recently I started working on severs/clusters for my biological analysis. I am struggling to find the operating system(OS) detail information before running my scripts. Can you please tell me how to find OS name using perl script?

Why the Perl script flash error and print weird lines once change the operating system?

Neel — Thu, 18 Jul 2013 10:52:41 -0500

Hi Bioinformatician, I am working on a small script which read a file and extract the gene coordinates. It works fine when I run on linux OS but in Window OS it print some weird sign, and also does not print the expected result. Following are the code for your reference.

#!/usr/bin/perl
use strict;
use warnings;

    my $fileIn = $ARGV[0];
    my $OutFile = $ARGV[1];
    open my $fh, '<', $fileIn or die "could not open $fileIn for read\n";
    open OUTFILE, ">" , $OutFile or die "$0: open $OutFile: $!";
    while (<$fh>) {
   chomp $_;
   my $line=trim($_);
   $line =~ s/(\.\.|\s+)/\t/g;
   $line =~ s/$|$/\t/g;
   my $number=$.;
   my @tmp=split /\t/, $line;
   if($tmp[2] ne 'complement') {
       my @newtmp = split(/gene/, $line);
       my $newline=$newtmp[1];
       my @tmp2=split /\t/, $newline;
       my $head="gene";
       print OUTFILE "$number\t$head\t\t$tmp2[1]\t$tmp2[2]\n";
       }
   else {
       print OUTFILE "$number\t$tmp[1]\t$tmp[2]\t$tmp[3]\t$tmp[4]\n";
       }
}

# Perl trim function to remove whitespace from the start and end of the string
sub trim($) {
   my $string = shift;
   $string =~ s/^[\t\s]+//;
   $string =~ s/[\t\s]+$//;
   return $string;
}