I have a set of 400 nucleotide sequences of plasmodium falciparum gene. Within this set I have to find out the variant nucleotide sequence of that particular gene. If it is a small number if sequences I can do it manually but with a large number how can I do this?
1) align the sequences using any multiple alignment tool like ClustalW, T-coffee, etc (its depends on your gene of interest)
2) identifying the variant nucleotide specifically
3) You can use MEGA software to calculate pair-wise nucleotide difference which will give you the Nucleotide sequence variants of that particular gene.
Hope this will help you.
You may use MEGA software to calculate pair-wise nucleotide/amino acid differences for your data set.
Use any alignment tool to find the differences between nucleotide sequences.
Use CLUSTALW server (http://www.genome.jp/tools/clustalw/) for your data set, and then select OUTPUT format CLUSTAL , this can help you identifying contiguous/variant region more specifically
Perform MSA using any Alignment tool.
http://www.ncbi.nlm.nih.gov/tools/cobalt/
http://www.ebi.ac.uk/Tools/msa/clustalw2/
Generic view
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http://www.ebi.ac.uk/Tools/msa/
1) align the sequences using any multiple alignment tool like ClustalW, T-coffee, etc (its depends on your gene of interest)
2) identifying the variant nucleotide specifically
3) You can use MEGA software to calculate pair-wise nucleotide difference which will give you the Nucleotide sequence variants of that particular gene.
Hope this will help you.
@Kaushik sir : yes thts wat i want., wid finding variants. for predicting Genetic Diversity ..Thanks a lot
Priyanka, that is really a good number of sequences. Your analysis will depend on the type of genetic region of P.falciparum. This means, you can perform different kinds of sequence analyses for genetic regions from coding/noncoding regions. Let me know if you need anyfurther help. All the best.
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