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Old 02-05-2010, 03:07 AM   #1
Location: Uppsala

Join Date: Jan 2010
Posts: 25
Default Steps to Genome Assembly??

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
~Adnan~ is offline   Reply With Quote
Old 02-05-2010, 07:31 PM   #2
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Location: los angeles

Join Date: Dec 2009
Posts: 2

I think this should answer some of your questions:

(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
tata is offline   Reply With Quote
Old 02-06-2010, 02:56 AM   #3
Location: Uppsala

Join Date: Jan 2010
Posts: 25

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?
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