Question: clustal w result interpretation
0
gravatar for dinesh
4.5 years ago by
dinesh50
India
dinesh50 wrote:

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 wether 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

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ADD COMMENTlink modified 4.4 years ago by Bara'a230 • written 4.5 years ago by dinesh50
1
gravatar for Bara'a
4.4 years ago by
Bara'a230
Amman - Jordan
Bara'a230 wrote:

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 ID's ) 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 :)

 
 
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Bara'a230
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