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Blast or mapper ?

Hello,

What are the advantages of using a homology research (such as blast) over a mapper (bwa, bowtie) ??

blast mapper
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updated by Antonio R. Franco Antonio R. Franco • written by Picasa Picasa

Blast is a similarity search, not homology search. And if you do not include your question to narrow it down to a specif problem, you will get all sorts of answers.

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written by h.mon h.mon

It is both, similarity and homology search. The success of BLAST relies not only on its speed but on its better model to assess statistical significance of similarities, i.e. whether a similarity (score) can be reached by chance or a common ancestry (homology) can be inferred.

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written by abascalfederico abascalfederico

I'm looking to classify me sequence (find which taxa are my sequences)

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written by Picasa Picasa

2 answers

That entirely depends on the application/purpose of course!

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written by WouterDeCoster WouterDeCoster

Indeed ... For example, if I'm looking to find from which species are my sequences ?

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written by Picasa Picasa

Either will work for that application. In fact, blasting a few reads at NCBI is the diagnostic tool of choice to answer your question (if you suspect that the data may be contaminated).

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written by GenoMax GenoMax

Ok, but what the advantages of using blast ?

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written by Picasa Picasa

It has a nice web application that allows you to just paste a few reads into and click a button. Also, you're going to have to spend a LOT of time to make an index of the size available from NCBI's public blast server.

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written by Devon Ryan Devon Ryan

Mappers are much more strict, they expect/look for near-exact matches between the reads and the genome. In contrast, BLAST allows you to look for distant homologies. Another difference is that with BLAST you can scan all known species in one run, whereas mappers expect one single genome.

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written by abascalfederico abascalfederico

Bowtie and BWA are designed for a different purpose. To align billions of reads to a reference genome or transcriptome To accomplish that, they index the reference, and then, reads are mapped very rapidly and efficiently

BLAST will need days, weeks or even more to do the same task

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written by Antonio R. Franco Antonio R. Franco

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