Question

Sequence Analysis of gene

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5.3 years ago

hfahad82 ▴ 10

Hello. I am a student. I am working on the mutational analysis of GJA8 gene. I want to know how to analyze my sequences to find any mutations

genome alignment sequence • 751 views

ADD COMMENT • link 5.3 years ago by hfahad82 ▴ 10

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What data do you have? - FASTQ files?
Which operating system do you use?
Do you understand Shell scripting?

ADD REPLY • link 5.3 years ago by Kevin Blighe 87k

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Yesh I have Sequence in FASTA and Text format. I am using MAC operating system.

ADD REPLY • link 5.3 years ago by hfahad82 ▴ 10

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Please use ADD REPLY/ADD COMMENT when responding to existing comments/posts to keep threads logically organized.

If this is an assignment question then please indicate so.

ADD REPLY • link 5.3 years ago by GenoMax 141k

score 1 · Answer 1 · 2018-12-31

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5.3 years ago

GenoMax 141k

You can find the reference sequence for GJA8 gene for the organism you are working with from NCBI (use RefSeq section when possible). Once you obtain the reference sequence in fasta format (download to your mac) you can use a pair-wise sequence alignment program to identify nucleotide positional differences between your sequence and the reference. (clustalW, MEGA. t-coffee are possible program examples). From then on it would be a matter of looking at translation of the sequence to identify functional consequences of the difference you see.