Smith-Waterman surprise

[tanas80]

Hello all, it is my first post on the seqanswers.com forum.

I am studying various alignment cases of Smith-Waterman algorithm.

I have tried the next two sequences for alignment:
>ref1
CAGGCT СТAAAАААСААААААССAAG GACTCG
>r1
CAGGCT СТАААААCAAAAACCAAG GACTCG

Surprisingly I get from http://www.ebi.ac.uk/Tools/psa/embos...ucleotide.html
an alignment with edited original sequences:

ref1               1 CAGGCTAAA-----AAGGACTCG     18
                     ||||||.||     |||||||||
read1              1 CAGGCTCAAAAACCAAGGACTCG     23

The most surprising thing is that flanks are intact, but middle part of sequences partially disappeared.

The result from http://insilico.ehu.es/align/ differs but also is shorter then source sequnces:

CAGGCTAAAAAGG-ACTC-G----  24
|||||| ||||   |         
CAGGCTCAAAAACCAAG-GACTCG  24

[dpryan]

Weird, you might just use R:

library(Biostrings)
read <- DNAString("CAGGCTCTAAAAACAAAAACCAAGGACTCG")
ref <- DNAString("CAGGCTCTAAAAAACAAAAAACCAAGGACTCG")
pairwiseAlignment(ref, read, type="local") #Default parameters
pairwiseAlignment(ref, read, type="local", gapOpening=-1) #Change gap penalties

The first one will yield

CAGGCTCTAAAAAACAAAAAACCAAGGACTCG
CAGGCTCTAAAAAC--AAAAACCAAGGACTCG

and the second one

CAGGCTCTAAAAAACAAAAAACCAAGGACTCG
CAGGCTCTAAAAA-CAAAAA-CCAAGGACTCG

since I changed the default gap penalties. You can also play with the match and mismatch penalties more easily than with the cumbersome (and slow) web interfaces. Remember that this is a local alignment, so you aren't guaranteed to get the full sequences in the output (try increasing the gapExtension penalty to -5).

[Galo]

Wow! This case and this information about R is great! Thank you two very much