Fórum de Discussão

Eu utilizei para achar a sequencia centro o mesmo algoritmo do EP1, e o score do EP2 eu considerei todo alinhamento com gap (-) -6.66 (gap - gap) 0 independente de ser no meio ou na extremidade da sequencia. Isso feito coluna por coluna e somando todos os valores.

Usando um exemplo meu
seqs
>AY425730
aggggaagggaccaaaa
>AY425731
aggggtttgtgaccaaaa
>AY425732
aggggaagaggacca

Resultado

/************************/
Sequencia 1 AY425730
Sequencia 2 AY425731
Sequencia 3 AY425732

Comparando Seq AY425730 Contra Seq AY425731 Score = 237.5
Comparando Seq AY425730 Contra Seq AY425732 Score = 229.5
Comparando Seq AY425731 Contra Seq AY425732 Score = 199.5
Sequencias com maior Score sao AY425730 e  AY425731 Com  Score:  237.5

Score do Alinhamento Global = 619
AY425730        -AGGGGAAG-GGACCAAAA
AY425731        AGGGGTTTG-TGACCAAAA
AY425732        -AGGGGAAGAGGACCA---
                       
/***********

Ja o clustal ficou
/******************

Sequence 1: AY425730         17 bp
Sequence 2: AY425731         18 bp
Sequence 3: AY425732         15 bp
Start of Pairwise alignments
Aligning...


Sequences (1:2) Aligned. Score: 41.1765
Sequences (1:3) Aligned. Score: 26.6667
Sequences (2:2) Aligned. Score: 38.8889
Sequences (2:3) Aligned. Score: 26.6667
Sequences (3:2) Aligned. Score: 26.6667
Sequences (3:3) Aligned. Score: 40
Guide tree        file created:   [clustalw.dnd]
Start of Multiple Alignment
There are 2 groups
Aligning...
Group 1: Sequences:   2      Score:237
Group 2:                     Delayed
Sequence:3     Score:213
Alignment Score 159
CLUSTAL-Alignment file created  [clustalw.aln]


clustalw.aln

CLUSTAL W (1.83) multiple sequence alignment


AY425730        -AGGGGAAGGGACCAAAA
AY425731        AGGGGTTTGTGACCAAAA
AY425732        AGGGGAAGAGGACCA---
                  ***     *****   

Até+...