Emboss: skipredundant vs needle

Question

[yarongeffen]

Hi, I’ve tried emboss skipredundant command (http://emboss.sourceforge.net/apps/cvs/emboss/apps/skipredundant.html) using the following two sequences:

>1
MMA
>2
MMG

Which of course have a similarity of 66.7%. But when running skipredundant with threshold 70% the sequences we’re still separated. How come?

Thanks

[GenoMax]

Is there a minimum length requirement that is coming into play?

[yarongeffen]

As far as I understand there is no minimum length requirement. When running needle command (http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needle.html) on the following two sequences:

>1
MMA

>2
MMG

I do get an output file with similarity of 66.7%.

I also tried skipredundant with threshold 70 on the following two 120 amino acid length sequences:

>1
MQSFLTLLKEHEDTCAPPAELVTLAGRLCRDFQDDLAQLQPLVTAILDSQLRLHLLDNADVALACARVLDQQEQQQAACRLLEGCQVPGGSQELVQLWNDIHYRLVMRRLGVAALTPVQK

>2
MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPGTQNF

and they got separated into two different files even though needle command output their similarity as 1.3%.

[yarongeffen]

Did anyone understand what was wrong?

[GenoMax]

What do you mean by they got separated into two files? If I try your example sequences only 1 sequence is kept.

$ skipredundant  -threshold 70 -redundant ""
Remove redundant sequences from an input set
Input sequence set: ju1.fa
Redundancy removal options
         1 : Single threshold percentage sequence similarity
         2 : Outside a range of acceptable threshold percentage similarities
Select number [1]: 
Gap opening penalty [10.0]: 
Gap extension penalty [0.5]: 
output sequence(s) [ju1.keep]: 

$ more ju1.keep 
>1
MQSFLTLLKEHEDTCAPPAELVTLAGRLCRDFQDDLAQLQPLVTAILDSQLRLHLLDNAD
VALACARVLDQQEQQQAACRLLEGCQVPGGSQELVQLWNDIHYRLVMRRLGVAALTPVQK

[yarongeffen]

GenoMax

I meant, if both of the sequences have a similarity of 1.3%, why only 1 sequence is kept? as I understand 2 of them should be kept because their similarity is below 70%

Thanks