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Recognizing patterns in DNA sequences.

Recognizing patterns in DNA sequences. - Biology Forum

Recognizing patterns in DNA sequences. - Biology Forums. Ask questions and discuss the study of Biology. If you have Biology questions from your homework ask them here!


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Old 11-03-2010, 10:20 AM
Pipette Filler
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Default Recognizing patterns in DNA sequences.



Hi all,

I am a computer scientist please dont fame me if this question sounds too simple to you. I'm aware that there are many software out there which allows you to search for fragments of DNA within a strand of sequences. Why do we need them? And how can we use these result? For instance

T T G C G A A A

I wanna find the motif of AAA with 100% threshold, in this instance position 6 - 9 would be my match, normally after researcher has the result what will he do to it? send it to BLAST?

Hope somebody can help me, thanks!

cheers,
Sam
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Old 11-03-2010, 09:07 PM
Pipette Filler
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Default Re: Recognizing patterns in DNA sequences.

For instance, an often searched fragment is the ATG start codon. This gives you information about amount and position of open reading frames (ORF). In higher context this gives you information about possible protein sequences. As you suggest such fragment searches are used for further database input. For example: I want to search an (specific) sequence pattern. With the expected results (your AAA) I search in blast if other species got the same pattern or not. The fragment can be searched for SNP (single nucleotide polymorphism), too. Another usage would be an alignment of this fragment with another one (for example primer design, phylogenetics). In a general summary I would say such fragment searches are searches for often classified motifs (ORF, Primer, ribosomal binding site, part of sequence, consensus sequences, transcription sites,...) wich gives you information about the properties and/or behaviour of your DNA sequence. I hope this answers this question as you expect, if not tell me.
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Old 11-03-2010, 09:10 PM
Pipette Filler
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Default Re: Recognizing patterns in DNA sequences.

By the way, I suggest this question would rather belong to the bioinformatics forum. I think there you would get more answers to such question type (computational science questions).
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