To retrieve gene name & function thorugh Genbank id (gi|9910297)

Thread Tools Search this Thread
Top Forums Shell Programming and Scripting To retrieve gene name & function thorugh Genbank id (gi|9910297)
# 1  
Old 08-11-2009
Java To retrieve gene name & function thorugh Genbank id (gi|9910297)

Hi ,
I have list of genbank id's and ref number in this format.

I want to retrive the gene name and fuction for each genbank list. I have around 1300 gi numbers in my excel sheet.

So anybody can help me to retrive the information from NCBI through perl script or any other package?

I can see the information through this link
for one by one..

Shibu John.
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Solaris

Zfs send & receive with encryption - how to retrieve data?

Good morning everyone, I'm looking for some help to retrieve data in a scenario where I might have made a big mistake. I'm hoping to understand what I did wrong. My system is made of two Solaris 11 Express servers (old free version for evaluation). The first if for data and the second is... (7 Replies)
Discussion started by: rnd
7 Replies

2. UNIX for Advanced & Expert Users

Map snps into a ref gene file

I have the following data set about the snps ID txt file POS ID 78599583 rs987435 33395779 rs345783 189807684 rs955894 33907909 rs6088791 75664046 rs11180435 218890658 rs17571465 127630276 rs17011450 90919465 rs6919430 and a gene... (7 Replies)
Discussion started by: marwah
7 Replies

3. Shell Programming and Scripting

awk to average target and gene

I am trying to modify the awk below to include the gene name ($5) for each target and can not seem to do so. Also, I'm not sure the calculation is right (average of all targets that are the same is $4 using the values in $7)? Thank you :). awk '{if((NR>1)&&($4!=last)){printf("%s\t%f\t%s\n",... (1 Reply)
Discussion started by: cmccabe
1 Replies

4. UNIX for Dummies Questions & Answers

Implement the '&&' function in a shell

Hello, I'm currently implementing the && function in a shell using C. For example, if we input cmd1 && cmd2, then cmd2 executes only when cmd1 exits successfully. I'm thinking about: int main() { int i; char **args; while(1) { printf("yongfeng's shell:~$ "); args =... (5 Replies)
Discussion started by: Yongfeng
5 Replies

5. Shell Programming and Scripting

login in wincvs thorugh shell or perl script

Hi , I am trying to write a script which does the wincvs login and does some checkout operations. When i do it from command prompt with command wincvs -d :pserver:username@server:/cvs/repository it pops up a cvs window and i can do some operations there. I wanted to automate this through... (1 Reply)
Discussion started by: namishtiwari
1 Replies

6. Shell Programming and Scripting

Extracting DNA sequences from GenBank files using Perl

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 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

7. Shell Programming and Scripting

GenBank Perl help...

Hey guys, I'm doing some Perl scripting for genomic data out of GenBank files...I have to extract the name of the plant, the file name, the number of bases, and all of the genes including their starting and ending positions...for example, with this GenBank file, LOCUS NC_010093 ... (7 Replies)
Discussion started by: akreibich07
7 Replies

8. UNIX for Dummies Questions & Answers

DNS forward and reverse entry required thorugh scripting instead of manually done

HI GUrus, I am very mcuh new for this forum ....i need you all guys help for resolving my queries. As i have DNS server , platform is sunsolaris----8. We are using that serevr for resolving all network nodes. I am going to explain the process what i am following .... I could have... (2 Replies)
Discussion started by: leenagoyal
2 Replies

9. Shell Programming and Scripting

retrieve a value from a function and assign it to a variable

hi i have a function. parse() { qname="lpdma111" qmgr="lpdma111" qalias="lpqqali" } Now the requirement is i want ot get the vaues form the function start() { //retireve the values from the parse function } (5 Replies)
Discussion started by: Satyak
5 Replies

10. UNIX for Dummies Questions & Answers

subshell & background function

Hello all, Can someone explain to me the advantage between using subshell over a function call in scripts? To me these are the same. Am I wrong to think this? (4 Replies)
Discussion started by: larry
4 Replies
Login or Register to Ask a Question
Ace::Sequence::Gene(3pm)				User Contributed Perl Documentation				  Ace::Sequence::Gene(3pm)

Ace::Sequence::Gene - Simple "Gene" Object SYNOPSIS
# open database connection and get an Ace::Object sequence use Ace::Sequence; # get a megabase from the middle of chromosome I $seq = Ace::Sequence->new(-name => 'CHROMOSOME_I, -db => $db, -offset => 3_000_000, -length => 1_000_000); # get all the genes @genes = $seq->genes; # get the exons from the first one @exons = $genes[0]->exons; # get the introns @introns = $genes[0]->introns # get the CDSs (NOT IMPLEMENTED YET!) @cds = $genes[0]->cds; DESCRIPTION
Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds the ability to retrieve the annotated introns and exons of the gene. OBJECT CREATION
You will not ordinarily create an Ace::Sequence::Gene object directly. Instead, objects will be created in response to a genes() call to an Ace::Sequence object. OBJECT METHODS
Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported: exons() @exons = $gene->exons; Return a list of Ace::Sequence::Feature objects corresponding to annotated exons. introns() @introns = $gene->introns; Return a list of Ace::Sequence::Feature objects corresponding to annotated introns. cds() @cds = $gene->cds; Return a list of Ace::Sequence::Feature objects corresponding to coding sequence. THIS IS NOT YET IMPLEMENTED. relative() $relative = $gene->relative; $gene->relative(1); This turns on and off relative coordinates. By default, the exons and intron features will be returned in the coordinate system used by the gene. If relative() is set to a true value, then coordinates will be expressed as relative to the start of the gene. The first exon will (usually) be 1. SEE ALSO
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF AUTHOR
Lincoln Stein <> with extensive help from Jean Thierry-Mieg <> Copyright (c) 1999, Lincoln D. Stein This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. POD ERRORS
Hey! The above document had some coding errors, which are explained below: Around line 148: You forgot a '=back' before '=head1' perl v5.14.2 2001-02-18 Ace::Sequence::Gene(3pm)