08-11-2009
To retrieve gene name & function thorugh Genbank id (gi|9910297)
Hi ,
I have list of genbank id's and ref number in this format.
gi|9910297|ref|NM_019974.1|
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
http://www.ncbi.nlm.nih.gov/nuccore/9910297
for one by one..
Shibu John.
10 More Discussions You Might Find Interesting
1. UNIX for Dummies Questions & Answers
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
2. Shell Programming and Scripting
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
3. UNIX for Dummies Questions & Answers
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
4. Shell Programming and Scripting
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
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. Shell Programming and Scripting
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
7. UNIX for Dummies Questions & Answers
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
8. Shell Programming and Scripting
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
9. UNIX for Advanced & Expert Users
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
10. Solaris
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
LEARN ABOUT DEBIAN
go::model::geneproduct
GO::Model::GeneProduct(3pm) User Contributed Perl Documentation GO::Model::GeneProduct(3pm)
NAME
GO::Model::GeneProduct - gene product in a particular species
DESCRIPTION
represents a gene product in a particular species (this will effectively always be refered to implicitly by the gene symbol even though a
gene may have >1 product)
acc
Usage -
Returns -
Args -
symbol
Usage -
Returns -
Args -
type
Usage -
Returns -
Args -
full_name
Usage -
Returns -
Args -
as_str
Usage -
Returns -
Args -
add_synonym
synonym_list
accessor: gets/set list of synonyms [array reference]
speciesdb
Usage -
Returns -
Args -
add_seq
Usage -
Returns -
Args - GO::Model::Seq
seq_list
Usage -
Returns - GO::Model::Seq listref
Args -
seq
Usage -
Returns - GO::Model::Seq
Args -
returns representative sequence object for this product
properties
Usage -
Returns - hashref
Args - hashref
set_property
Usage - $sf->set_property("wibble", "on");
Returns -
Args - property key, property scalar
note: the property is assumed to be multivalued, therefore
$sf->set_property($k, $scalar) will add to the array, and
$sf->set_property($k, $arrayref) will set the array
get_property
Usage -
Returns - first element of the property
Args - property key
get_property_list
Usage -
Returns - the property arrayref
Args - property key
to_fasta
Usage -
Returns -
Args -
returns the longest seq by default
perl v5.14.2 2013-02-07 GO::Model::GeneProduct(3pm)