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Seqeunce alignment

Seqeunce alignment - Bioinformatics

Seqeunce alignment - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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  #1  
Old 03-21-2011, 05:29 PM
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Default Seqeunce alignment



I am having trouble processing some alignment data using the packages i normally use (BioEdit and MEGA) and was hoping that others can suggest a better tool to do the following

1) I have a list of 100+ seqeunces from very closely related species which i want to use to look for natural SNP thus suggesting where mutation is least detrimental. What i would like is a tool that i can put these seqeunces in and it can collapse the 100+ seqeunces into groups e.g. group one is 100% identical to my reference, group 2 is 99% identical but has an A to T change at position XXX etc i am thinking this may be similar to RNAseq type work so theres probably a tool in that field which i am unaware of.

2) The list of 100+ sequences includes about 4000bp which have been aligned with ClustalW and now i want to divide it up into segment each containing just one CDS of the operon so i can look at these indivudally - is there a tool which will allow me to select part of an alignment and copy this into a new file
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Old 03-25-2011, 05:10 AM
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Default Re: Seqeunce alignment

Try UGENE ([Only registered users see links. ])

1) It does not support results grouping (however idea is good, we will add it to the feature list), but it visual editor integrates a lot of alignment algorithms: muscle, kalign, clustal, mafft, tcoffee. So you can try different alignment programs and see the results

2) Use 'Edit -> Extract selection to MSA' alignment editor context menu in version 1.9.2 and lower and 'Export -> Save selection' in 1.9.3+
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Old 05-08-2011, 11:07 AM
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Default Re: Seqeunce alignment

Yeah Ugene will work best in your case.
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Old 01-06-2012, 05:11 PM
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Default Re: Seqeunce alignment

i am very new to bioinformatics, would you guys briefly tell me what exactly software UGene do?
Does not check for introns for genes? Can i draw the secondary structure or rRNAs?

thanks

Last edited by bbsinfo; 01-06-2012 at 05:12 PM.
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