Question

how to improve multiple sequence alignment by removing outlier sequence ?

2

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7.7 years ago

Pei ▴ 170

Hi all:

Have you tried to remove outlier sequence after constructing a multiple sequence alignment ? Is there any recommended tools for this aim ?

Thanks in advance! Best,

alignment • 2.7k views

ADD COMMENT • link updated 4.9 years ago by Biostar 20 • written 7.7 years ago by Pei ▴ 170

0

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What type of sequence: protein, nucleotide or others?

ADD REPLY • link 7.7 years ago by Khader Shameer 18k

score 1 · Answer 1 · 2016-07-23

1

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7.7 years ago

Erik Wright ▴ 420

Jehl, P., Sievers, F., & Higgins, D. G. (2015). OD-seq: outlier detection in multiple sequence alignments. BMC Bioinformatics, 1–11. http://doi.org/10.1186/s12859-015-0702-1

ADD COMMENT • link 7.7 years ago by Erik Wright ▴ 420

score 1 · Answer 2 · 2016-10-20

Jalview (www.jalview.org) is a good visualisation workbench for multiple sequence alignments. It has some useful tools for selecting, editing, hiding and grouping sequences, check out this video playlist. When used in combination with the MSA services, it is a great way to interrogate your alignment, as illustrated in this video at about 3.57.