blastn for short sequences against a genome

Question

[sinduri_1312]

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?

[Prasad]

u could use bowtie or SHRiMP (has specific alignment parameters for small RNA) for aligning miRNAs. If you still want to use blastn, try changing the -task option to blastn-short.

http://genomespot.blogspot.in/2014/11/microrna-aligners-compared.html

This might help to choose an aligner

[sinduri_1312]

thank u 4 d reply....vl try ur advise.

[sinduri_1312]

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

[Prasad]

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

[sinduri_1312]

it is a reference genome

[sinduri_1312]

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

[Prasad]

[e-mail]

Answer 1

[Antonio R. Franco]

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

[sinduri_1312]

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

[Antonio R. Franco]

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

[sinduri_1312]

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

[Antonio R. Franco]

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