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Finding unknown DNA repeat sequence

Finding unknown DNA repeat sequence - Bioinformatics

Finding unknown DNA repeat sequence - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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  #1  
Old 06-13-2009, 12:21 AM
Pipette Filler
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Post Finding unknown DNA repeat sequence



Hi Everyone,

I work with molecular biology and I need to find some unknown DNA repeat sequence in a pdb file from NCBI. My question is, is there some program that searches through large sequences and finds out large chunks of repeat sequences and lets me know what the sequence(s) is(are).

I've been looking for a free program that would perform an algorithm to find the unknown DNA repeat sequences(tandem or not) but could not find anything. If anyone knows of any free program/site please let me know.


Thank you.
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Old 06-26-2009, 05:45 PM
Pipette Filler
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Default Re: Finding unknown DNA repeat sequence

emboss.sourceforge.net/apps/release/6.0/emboss/apps/nucleic_repeats_group.html

repeat-match and extact-tandem in mummer.sourceforge.net/manual

I am not allowed to have URL in the text.Those link are URL with usual http prefix.
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Old 07-25-2009, 02:52 PM
Pipette Filler
 
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Default Re: Finding unknown DNA repeat sequence

Hello
For searching tandem repeat (mini and microsatellites), I have used a free software called (e-Tandem), you can find it Pasteur institute website by Google it as (mobyle pasteur etandem), It is good software but it is slightly slow and does not do for very large sequences. If you have a large sequence; you have to chop it into parts.
Sarwat65
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dna , dna repeat , finding , repeat , sequence , sequences , unknown


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