SHRiMP mapping algorithm

[neha]

Hello everyone,

I have miRNA data generated through ION PGM. I am using SHRiMP software for mapping. I want to know how exactly SHRiMP algorith works

It is written that by default it makes 3 seeds with weight 12
seed1: 11110111101111
seed2: 1111011100100001111
seed3: 1111000011001101111

1. I want to know if this is the only pattern it makes seeds or it makes seed
according to our data.
2. Now will it match all the seeds and in what order. If out of three two seeds match and one does not match then will it consider that seed or will it be discarded.

3. when is the extension of these seeds take place??

Hoping for a positive response.

Neha

[Laurent Noé]

Hi Neha,

sorry for this "too late (~ one year) " answer :

(a) first, note that there is a "--mode mirna" in SHRiMP that can help in your work ?
(b) be careful with homopolymers ... if too many of them, as they generate indels on ION, they will "break" the seeds; however, i hope that your sequences are "homopolymer-free" (miRNA ?)



1. seeds are fixed (and the ones you show in your post are btw adapted for SOLiD read mapping ...), so they will not change, but you can specify others before running the tool ...

=> if you have some miRNA, may be the following (from the "nucleotide" version of the SToRM read mapper)
1111001010011001111
1111100111010111
11101101111111
would help ?

2. no matter the order of the seed shapes is : as far as i remember, in SHRiMP you need "two hits" (-n 2) of two seeds (either the same seed shape at two different positions, or two different shape even at the same pos) to trigger an alignment ;

there is a good tutorial too in
http://compbio.cs.toronto.edu/shrimp/README
starting with "Filter 1: Window Generation"

dont forget to play with the score threshold -v and -h with smaller percentages ... decreasing them can help too.

3. this seems to be a "double hit (by default)" and " -w 140% read alignment" :
see the "Filter 2: Vector SW/Ungapped Alignment" section for more details

Hoping this answers some of your questions ? (sorry for the "see the ref manual, but seems that even helped me :-) )

Have a nice day

L.