Extract Sequence From The Genome?

[chayan]

Hi,

I have extracted a population genome bins from a metagenome..now i want to give a taxonomic position to that bin..for that matter multiple sequence based tree will be helpful..can any one please suggest, that suppose if i want to extract ~26 conserved genes from ~ 50 genomes (gene-bank file)how to do that..i mean with bio-python or any other way?? any script to extract multiple sequences from a gene-bank file will be really helpful..


Thanks in advance...

[chayan]

Hii every one..can any one help me with this problem???

[gsgs]

I can probably do it in windows/dos , you have the position of the genes ?
fasta file ?
Or you send the file I send the result ?
or part of it, to see/test it and I send the program

[chayan]

that will be awesome...you want me to send the gbk file along with the list of genes that i want to extract from the gbk??? then please give me ur mail id...i can send you the gbk files or the NCBI Genebank accession numbers...

[chayan]

as i am not sure that my reply to your message has been sent properly or not (due to network failure) thats why i am pasting it here also...

from the metagenomic bin i have extracted the 16s rRNA and based on the BLAST result i have selected ~50 genomes to compare my bin because merely based on 16s result phylogenetic conclusion will not be ideal...that's why i want to generate a concatenated multi loci tree of 26 universally present conserved genes..i am looking forward for a method to extract those genes of interest in one go..manual extraction will be too much time consuming...i hope now the problem is clear to you..

yes its gene bank format...i understand 50 gbk files will take a lots of space..in that case i can send you the accession numbers only..

or else if you can guide me to solve this..

even me too...in that case I will send you the files of gbk numbers and the gene list with 1-2 days..

if you want anything more to clarify please do tell me..

thanks

[gsgs]

find appearances of a certain subsequence in the long sequences of the file and extract the
next xxx bytes starting at that position (or some yyy bytes before or after it)

would that do it ?

[gsgs]

he wants to extract from the genbank records (files *.gbk , *.gb ?) not only the amino-acid sequences
of the genes, as they are typically in those records, but also the corresponding nucleotides.

Is there a tool, that does this ?