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blastn for short sequences against a genome

how to perform blastn for short sequences such as miRNA against a genome? i have tried by changing expect threshold, word size but still gives me error. i have even tried using bioedit, but all in vain. it gives me the message 'no hits found'. also i have done local blast and here even it shows me 'no hits found'. what should i do....please can someone guide me?

blast mirna blastn local blast bioedit
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updated by Antonio R. Franco Antonio R. Franco • written by sinduri_1312 • sinduri_1312

the genome i am working with is of Ictidomys tridecemlineatus(13 lined ground squirrel). vl bowtie give results regarding dis genome?

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written by sinduri_1312 • sinduri_1312

Is it the exact reference or closest?? Anyway i can get the results by adjusting different parameters of bowtie

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written by Prasad Prasad

need some more guidance on dis...can i have ur e-mail id?

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written by sinduri_1312 • sinduri_1312

msprasad693@gmail.com

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written by Prasad Prasad

1 answer

Another possibility is using a mapper such as bowtie

There are two versions of bowtie. Bowtie1 and Bowtie2

Bowtie1 has better resolution and give more details when query is very short

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written by Antonio R. Franco Antonio R. Franco

thanks a lot sir....going to work wid bowtie now.

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written by sinduri_1312 • sinduri_1312

Just a note

Bowtie will give you a SAM file with extra information

  • you can see the alignment sequence with no or with some mismatches. This will be indicated in the NM:i:X field, where X is the number of mismatches

    • You can see if the alignment will take place in the plus or minus strand (the reverse strand). See the 0 or 16 value in the second field

    • You will need to enter into the SAM specification file to get the most of it

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written by Antonio R. Franco Antonio R. Franco

the genome i am working with is of Ictidomys tridecemlineatus(13 lined ground squirrel). vl bowtie give results regarding dis genome?

• 1 views • link
written by sinduri_1312 • sinduri_1312

You need a reference sequence to align. And this is all..

Yo are required to read and follow bowtie instructions, but believe me that it is worth to do it in your case, because you can get fully aligned sequences and places where some minor mismatch can be of interest

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written by Antonio R. Franco Antonio R. Franco

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