Proteins

varsha raja rnavarsha at yahoo.com
Wed Oct 9 22:07:32 EST 2002


This can be definately implemented in High throughput
database blasting and beauty of Perl is ,it is more
stronger than any other language.It is rather more
powerful where you need to go for SOP and database
modeling....it is useful when you need to screen a
very large amount of data and filters are required
till teriary level....for proteins....
thanks,

VARSHA RAJA
(New Delhi)


--- Marcus Davy <MDavy at hortresearch.co.nz> wrote:
>  Yo,
>  This program is written in perl,
>  It is a command line driven simple script to run
>  each protein sequence
>  in order and create an output file.
>  This cannot easily be implemented into the
>  bioinformatics webbased blasting facility.
>
>  marcus
>

--- varsha raja <rnavarsha at yahoo.com> wrote:
>  Dear Arabidopsis Group Users:
>
>  Sachin Gandhi and Varsha Raja
>
>  We have designed a new small programme if someone is
>  interested to blast multiple protein sequences
>  together.
>
>  Input should be a file containing multiple protein
>  sequences in FASTA format.
>
>  #### Programme starts:
>
>
>  print ("Enter input file Name : ");
>  chomp($FileName = <STDIN>);
>
>  print ("Enter Output file name :");
>  chomp($OutFile = <STDIN>);
>
>  print "Process Started...\n";
>
>  open (READ,"<$FileName") or die "Cannot open input
>  file : $FileName\n\n";
>  open (WRITE,">$OutFile") or die "Cannot open output
>  file : $OutFile\n\n";
>
>  while (<READ>)
>  {
>  	chomp($Line = $_);
>
>  	if ($Line !~ /\>^/)
>  	{
>  		$Line =~ s/\s+|[1-9]+//ig;
>  		print WRITE $Line;
>  	}
>  }
>
>  close (READ);
>  close (WRITE);
>
>  print "Process Completed...\n\n";
>
>
>  #### Programme ends.
>
>
>  Many thanks,
>  Sincerely,
>  VARSHA
>
>
>
>  =====
>  Varsha Raja,Faculty, Bioinformatics,Xintra, Suite#
>  600
>  55,Scarborough Town Centre
>  Court,Toronto,OntariM1P4X4,CANADA
>  Voice: 1-416-290-6044,Fax: 1-416-290-6110 , Personal
>  SMS-Box Address
>  is: http://mobile.icq.com/166604110
>  Web:http://xintra.dhs.org/varsha.html
>  "Om Bhurbhurva Swah! Tasta Viturva Renya
>     Bhargo,Devatsya,Dhimahi,Dhiyoyonaha
>  Prachodayata!"
>
>  __________________________________________________
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>  ---


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