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Find contentAbout Me
I am a human being in constant evolution, powered by ATP hydrolisis, and some food!
Community Stats
- Group Active Members
- Active Posts 53
- Profile Views 6,898
- Member Title Enthusiast
- Age 33 years old
- Birthday November 2, 1979
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Gender
Male
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Location
México
About me
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My research interests
Biochemistry, Signal transduction, Molecular Biology, Molecular Evolution, Bioinformatics, Biotechnology, Systems Biology.
Posts I've Made
In Topic: Looking for a method to filter out data from related BLAST results
20 June 2012 - 07:15 PM
Try a blast parser, galaxy has a nice one and what about doing phylogenetic analysis from your blast results, and then you can compare the trees
In Topic: What test should I use?
06 June 2012 - 07:13 PM
May be you need a post hoc test, like Dunnet for comparing every group against the control, or the tukey test to compare every group of your samples.
you could try to post this question to http://stats.stackexchange.com with some sample data
you could try to post this question to http://stats.stackexchange.com with some sample data
In Topic: What test should I use?
30 May 2012 - 05:47 PM
You should try repeated mesures AOVA
In Topic: How to use NCBI ?
24 May 2012 - 08:54 PM
The E- value tells you the probability to get a random match, so you must consider the lowest values.
In other words, for gene prediction you wanna predict all the binding sites for regulatory elements, like transcription factors, activators, repressors, etc.. Sometimes this is a difficult task, but proteins, are built with a limited number of blocks (signature, motif), so it's relatively easy to look for known blocks, at databases builded for that purpose.
If you wanna get blast results for proteins, you should use blastx against swissprot.
This online training material could help you a lot, to grasp the blast basics http://bioinfbook.or...pter4/index.php from
Bioinformatics and Functional Genomics book, one of the best Bioinformatics books, I have read.
@FelipeRiveroll
Quote
"Also if you do not need to look for regulatory elements in DNA, it's easier to work with proteins, they have signature conservation and protein families, that help you to infer protein function for unknown sequences.".
In other words, for gene prediction you wanna predict all the binding sites for regulatory elements, like transcription factors, activators, repressors, etc.. Sometimes this is a difficult task, but proteins, are built with a limited number of blocks (signature, motif), so it's relatively easy to look for known blocks, at databases builded for that purpose.
If you wanna get blast results for proteins, you should use blastx against swissprot.
This online training material could help you a lot, to grasp the blast basics http://bioinfbook.or...pter4/index.php from
Bioinformatics and Functional Genomics book, one of the best Bioinformatics books, I have read.
@FelipeRiveroll
In Topic: How to use NCBI ?
23 May 2012 - 10:36 AM
Hi lyok
Mabe you're looking for a blast parser like this http://kirill-kryuko...s/blast-parser/ to get chromosome locations, in a simple output. And also see this post http://www.biostars....rom-the-genome/
I think you should consider the E-value instead of similarity, for homology prediction. Also if you do not need to look for regulatory elements in DNA, it's easier to work with proteins, they have signature conservation and protein families, that help you to infer protein function for unknown sequences.
Mabe you're looking for a blast parser like this http://kirill-kryuko...s/blast-parser/ to get chromosome locations, in a simple output. And also see this post http://www.biostars....rom-the-genome/
I think you should consider the E-value instead of similarity, for homology prediction. Also if you do not need to look for regulatory elements in DNA, it's easier to work with proteins, they have signature conservation and protein families, that help you to infer protein function for unknown sequences.
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