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Old 02-05-2010, 03:07 AM   #1
niazi84@hotmail.com
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Default Steps to Genome Assembly??

Hello,
I am a newbie to genome assembling. Can anybody help me knowing because i am gone mad after reading about assembly and alignment in articles but couldn't get anything out. My main questions related to this are:

What is difference between assemblers and aligners?
When alignment is done in assembling?
What is the difference between contigs and consensus sequence?

In simple words what are the working steps/flow of genome assembling? Thanks in advance
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Old 02-05-2010, 07:31 PM   #2
tata
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I think this should answer some of your questions:
http://www.cbcb.umd.edu/research/assembly_primer.shtml

Also,
(from wikipedia):
...a sequence alignment is a way of arranging the sequences of DNA, RNA, or Protein to identify regions of similarity ... between the sequences.

Sequence alignment is also a part of genome assembly, where sequences are aligned to find overlap so that contigs (long stretches of sequence) can be formed.

hope it helps
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Old 02-06-2010, 02:56 AM   #3
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Thans tata,

its good reference. I used Maq for assembly today and got the consensus sequence finally in .cns file. Now what should be done next to refine the sequence and which tools, any idea?
Thanks
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