/sci/ - Science & Math

[Anonymous No.3813871]

If I'm looking for a novel gene (uncharacterized in a particular organism), and someone has already done the work for me (>9000 ESTs on ncbi), how do I search for homologous regions on model organisms (that have known function), to try and characterize the one I'm looking for?

In other words: Huge EST database for this organism, how do I analyze it, barring BLASTing every one individually?

[Anonymous No.3813912]

bump

[Anonymous No.3813960]

[Anonymous No.3814010]

Well sorry man. I'm sad to see this die, since it's actual science, but I don't know how to help you. I've done work in this field, but only briefly, and I don't know how to help you find matches. Sorry.

[Anonymous No.3814078]

[Anonymous No.3814813]

[Anonymous No.3814849]

My face when someone asks an actual scientific question on /sci/

[Anonymous No.3815281]

[Anonymous No.3815335]

What is wrong with Blast, OP? Ensembl will blow your mind. Use the right parameters. It might take you a week or so. Blasting against a translated database (tblastn/tblastx) may lead faster to result. There is some specialized blast output page for cross-species results, I forgot the name.

You also could do a hybridization screen on a phage library.

Or just do RT-PCR on your organism of interest, maybe with degenerated primers.

[Anonymous No.3815353]

you work with c. elegans OP?

[Anonymous No.3815360]

>>3815353
Well, I'm trying to use c. elegans as a resource since so much is known about it.

So, if I have 500+ pages of ESTs from my organism, how do I look for c. elegans homologs is my question, is there a tool for that?

Say I want to look for hypothetical elegans gene TES-1; how do I search through my organisms ESTs for homology?

[Anonymous No.3815386]

>>3815360
so, you got 500 ESTs from a strange organism (which name you don't reveal?), and you want to identify those ESTs who have a close relative in elegans?

[Anonymous No.3815392]

>>3815386
Yep. but not 500, over 12,000.

[Anonymous No.3815401]

>>3815392
write some biopython script that uses blast.

[Anonymous No.3815405]

To be more particular, I know of a family of genes that I would very much like to try and modify, if they exist in my organism. However, very little genetic work has been done on this thing, so not a lot is known about it (except this paper that started work, and got all these ESTs from different stages of the life cycle).

[Anonymous No.3815412]

usually those annotations are somehow automatically done by the people working at ncbi. they use hiddenmarkov and shit to do genpept hierarchy trees and so.

[Anonymous No.3815425]

It's somehow possible to put all those ESTs into a custom database searchable by NCBI blast. This would be how you could search with the sequence of e.g. Wnt or Hox against your organism's 12.000 ESTs.

[Anonymous No.3815449]

>>3815425
That would be exactly what I'm trying to do. I have about 40 genes that I'd need to do it with (these genes knocked out with silencing RNAs give me the phenotype I'm looking for).

[Anonymous No.3815477]

>>3815449
If I wanted to do this kind of shit, I'd ask the NCBI helpdesk to assemble this novel organism's EST blast database from my data. I'm sure they would do this assembly for you or provide you with the info necessary.

http://puneetwadhwa.blogspot.com/2005/10/creating-and-using-custom-blast.html

[Anonymous No.3816107]

>>3815477
Excellent, thanks anon.

[Anonymous No.3816122]

>>3815449

>these genes knocked out with silencing RNAs give me the phenotype I'm looking for

Without going to much into it (don't want to breach any contracts) what phenotype are you looking at?

[Anonymous No.3816139]

>>3816122
tra related.

[Anonymous No.3816158]

>>3813871
you should take a bioinformatic course bro.


That organsism that you have...
do you have its genome?
or you just want to find the THAT GENE (cds or part of the gene i dunno) with some experiments?

[Anonymous No.3816228]

>>3816158