clustal w result interpretation

Question

[dinesh]

I used microrna in clustal w software to remove redundancy . some part of output was like this ..can any one tell how to interpret the results ..... what is that score. how can I know whether the redundancy is removed

Sequences (1:2) Aligned. Score:  36
Sequences (1:3) Aligned. Score:  19
Sequences (1:4) Aligned. Score:  18
Sequences (1:5) Aligned. Score:  22
Sequences (1:6) Aligned. Score:  52
Sequences (1:7) Aligned. Score:  40
Sequences (1:8) Aligned. Score:  22
Sequences (1:9) Aligned. Score:  54
Sequences (1:10) Aligned. Score:  18
Sequences (1:11) Aligned. Score:  40
Sequences (1:12) Aligned. Score:  36
Sequences (1:13) Aligned. Score:  13
Sequences (1:14) Aligned. Score:  31
Sequences (1:15) Aligned. Score:  45
Sequences (1:16) Aligned. Score:  36
Sequences (1:17) Aligned. Score:  36
Sequences (1:18) Aligned. Score:  45
Sequences (1:19) Aligned. Score:  40
Sequences (1:20) Aligned. Score:  31
Sequences (1:21) Aligned. Score:  45
Sequences (1:22) Aligned. Score:  31
Sequences (1:23) Aligned. Score:  50
Sequences (1:24) Aligned. Score:  31
Sequences (1:25) Aligned. Score:  36
Sequences (1:26) Aligned. Score:  36
Sequences (1:27) Aligned. Score:  50
Sequences (1:28) Aligned. Score:  31
Sequences (1:29) Aligned. Score:  50
Sequences (1:30) Aligned. Score:  23
Sequences (1:31) Aligned. Score:  54
Sequences (1:32) Aligned. Score:  23
Sequences (1:33) Aligned. Score:  63
Sequences (1:34) Aligned. Score:  36
Sequences (1:35) Aligned. Score:  63
Sequences (1:36) Aligned. Score:  18
Sequences (1:37) Aligned. Score:  54
Sequences (1:38) Aligned. Score:  27
Sequences (1:39) Aligned. Score:  40
Sequences (1:40) Aligned. Score:  40
Sequences (1:41) Aligned. Score:  54
Sequences (1:42) Aligned. Score:  45
Sequences (1:43) Aligned. Score:  50
Sequences (1:44) Aligned. Score:  54
Sequences (1:45) Aligned. Score:  36
Sequences (1:46) Aligned. Score:  36
Sequences (1:47) Aligned. Score:  27
Sequences (1:48) Aligned. Score:  18
Sequences (1:49) Aligned. Score:  18
Sequences (1:50) Aligned. Score:  18
Sequences (1:51) Aligned. Score:  50
Sequences (1:52) Aligned. Score:  36
Sequences (1:53) Aligned. Score:  36
Sequences (1:54) Aligned. Score:  27
Sequences (1:55) Aligned. Score:  40
Sequences (1:56) Aligned. Score:  45
Sequences (1:57) Aligned. Score:  18
Sequences (1:58) Aligned. Score:  45
Sequences (1:59) Aligned. Score:  27
Sequences (1:60) Aligned. Score:  31

Answer 1

[Bara'a]

The sample you provided represents the pairwise alignment performed on the data set.

The pairwise alignment score is simply the number of identities between the two sequences divided by the length of the alignment and represented as a percentage, while the multiple alignment score is the sum of pairwise scores.

You can refer to this for more detailed answers: http://people.scs.carleton.ca/~dehne/publications/2-68.pdf

Regarding the redundancy , clustalW2 initially performs the pairwise alignment on all pairs of sequences given in the data set (identified by IDs) NOT WRTO order ... by which I mean aligning every single sequence with all other existing sequences, excluding sequences against themselves, e.g. (1:1), (2:2), (3:3) etc ... and same sequences of different order , i.e say we have sequences 2 and 3 (2:3) V.s. (3.2) done only once by which appears first.

This is normally done by clustalW2 unless you have duplicates in the original data set, in which two identical sequences have two different ID's ... in this case you have to filter out your sequences to have them unique, for this purpose check this out: How To Remove The Same Sequences In The Fasta Files?

Hope you find this useful :)