Homologous Sequence
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9.1 years ago

Hi,

I have a set of proteins and I need to search homologous partners for them. I wanted to automate the process of searching and I wrote a perl script for that. Now, the question is what should be the % of identity (both min and max) should I use in searching the homologous sequences. Also, the database that I using for blastp is PDB , since I need the structures only .. Kindly help out with this problem ??

Regards, BHARAT

sequence • 4.4k views
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Please take care with the word "homologous". It has a very specific meaning which you should understand.

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The PID that you choose varies for different purposes. Give us more details about your problem for answering your question.

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My query is that I want to obtain homologous protein structures for my dataset ?? . Since the dataset is large I need some sort of cutoff values to identify the homologous sequences

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You can use Dali to make the identity scores from structural alignments.

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9.1 years ago
qiyunzhu ▴ 430

I recalls that 30% is an empirical cutoff in term of protein sequence similarity.

If you use BLAST, then E-value serves as a better indicator of homology, comparing to identity. Because E-value takes into account the lengths of query and subject sequences. For example, a short protein is more likely to be somehow similar to another random guy simply by chance, in which case, a high E-value speaks stronger than a high identity. As I know there's no standard cutoff for E-value. You can try from 1e-2 (IMG's protocol) to 1e-10 or even lower.

On the other hand, there are a bunch of programs to help you identify orthologs, using more sophisticated algorithms, such as OrthoMCL. You can try those...

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E-values give a measure of similarity, not homology...

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I know. But is there a better and practical way to measure "homology"?

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I know what you mean. Homology is hard to show in a "high-throughput" manner. Just wanted to clarify for everyone reading the post!

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You are right. Thanks for clarifying that!

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