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Old 06-12-2013, 10:00 PM   #1
Felix0902
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Default What are the differences between alignment, mapping, and assembly in Bioinfomatics?

What's the differences between alignment, mapping and assembly in Bioinfomatics?
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Old 06-12-2013, 11:45 PM   #2
maubp
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It sounds like a good homework question to me - something you could start to answer by searching the literature with those keywords for some review papers perhaps?
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Old 06-19-2013, 05:32 AM   #3
syfo
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You could even start by typing "sequence alignment", "read mapping" and "sequence assembly" in some internet search engine.
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Old 06-28-2013, 12:19 PM   #4
amarth
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Alignment is the comparison between sequences (nucleic acids or aminoacids), the result will be some common letters within their sequence structures.
For example, you have this two sequences of letters:

ABCDEFGHIPQRSVXZ
ACCHJKLPQTXYZ

Then you want to align them, to look for similar 'features'. A program will do the work (like Clustal) The result will be:

ABCDEFGHI---PQRSVX-Z
ACC-----HJKLPQT--XYZ

This is what is called Alignment.
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Old 06-28-2013, 12:21 PM   #5
prs321
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Quote:
Originally Posted by syfo View Post
You could even start by typing "sequence alignment", "read mapping" and "sequence assembly" in some internet search engine.

Or you could just answer his or her question.
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Old 06-28-2013, 04:00 PM   #6
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In general, don't expect people to spend much time answering your question if your question doesn't demonstrate that you have spent some time trying to figure it out for yourself.

You spend 10 seconds writing that? Don't expect anyone to spend 10 minutes answering you.

The 10 second answer: mapping and alignment are the same. You compare your reads to a known reference. Assembly is when you take reads and build contigs solely by looking at the reads, with no reference.
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Old 07-15-2013, 02:24 AM   #7
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Hello, I have a similar question like but regarding mapping and Assembly. From literature, I have seen that there are 2 types of assemblies - denovo and assembly against a reference. The problem is that I do not understand the difference between mapping assembly and mapping reads against a reference. I expect that mapping assembly produce a set of contigs since it is assembly. From literature, these terms are confusing. Can anyone direct me towards a paper and give me some explanations on that.

Thank you.
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Old 07-15-2013, 02:50 AM   #8
rhinoceros
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Quote:
Originally Posted by pari_89 View Post
Hello, I have a similar question like but regarding mapping and Assembly. From literature, I have seen that there are 2 types of assemblies - denovo and assembly against a reference. The problem is that I do not understand the difference between mapping assembly and mapping reads against a reference. I expect that mapping assembly produce a set of contigs since it is assembly. From literature, these terms are confusing. Can anyone direct me towards a paper and give me some explanations on that.

Thank you.
The way I see it:

De Novo Assembly = Contigs are strictly determined from the overlap of reads

Assembly against a reference = Reads are mapped against a known genomic sequence, contigs are build afterwards with this added information
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Old 07-15-2013, 09:41 AM   #9
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Mapping reads is entirely different. Mapping is taking one read at a time, looking at a genome, and figuring out where that read best goes.

Assembly is taking a bunch of reads together, and building contigs. You can either do this entirely de novo, or you can use a reference for guidance.
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Old 07-25-2013, 07:39 PM   #10
ahmad87
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Quote:
Originally Posted by swbarnes2 View Post
In general, don't expect people to spend much time answering your question if your question doesn't demonstrate that you have spent some time trying to figure it out for yourself.

You spend 10 seconds writing that? Don't expect anyone to spend 10 minutes answering you.

The 10 second answer: mapping and alignment are the same. You compare your reads to a known reference. Assembly is when you take reads and build contigs solely by looking at the reads, with no reference.
This is the whole point of a forum (also searching and to some extent even internet), you ask questions and people who have time will answer you!!! Nobody has forced you to answer if you don't have time!
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Old 07-25-2013, 11:59 PM   #11
maubp
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Quote:
Originally Posted by ahmad87 View Post
This is the whole point of a forum (also searching and to some extent even internet), you ask questions and people who have time will answer you!!! Nobody has forced you to answer if you don't have time!
Not exactly - if you ask specific well researched questions, yes. Otherwise you are just adding noise making it harder for everyone (it wastes time for the people who might be able to advise you, and it wastes time for other beginners by adding another unhelpful search result to the forum).

I suggest reading:

[1] Dall'Olio GM et al. 2012: Ten simple rules for getting help from online scientific communities http://www.ploscompbiol.org/article/...l.pcbi.1002202

[2] Eric Steven Raymond: How to ask questions the smart way http://www.catb.org/esr/faqs/smart-questions.html

[3] Normandeau et al: Tutorial: How to ask Good Questions on Technical and Scientific Forums
http://www.biostars.org/p/75548/
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Old 09-23-2014, 04:48 AM   #12
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Quote:
Originally Posted by swbarnes2 View Post
The 10 second answer: mapping and alignment are the same. You compare your reads to a known reference. Assembly is when you take reads and build contigs solely by looking at the reads, with no reference.
That's all that is needed - thank you for answering the question.

The literature around alignment and mapping uses a lot of terms interchangably, so in my mind this is a fair question. You might think this is simple if you have been involved in the evolution and development of the discipline, but as a relative newcomer I see that almost none of the terms are used consistently throughout, which causes a lot of confusion.
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Old 09-23-2014, 05:30 AM   #13
rhinoceros
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Quote:
Originally Posted by Jegar View Post
That's all that is needed - thank you for answering the question.

The literature around alignment and mapping uses a lot of terms interchangably, so in my mind this is a fair question. You might think this is simple if you have been involved in the evolution and development of the discipline, but as a relative newcomer I see that almost none of the terms are used consistently throughout, which causes a lot of confusion.
In my opinion mapping and alignment are not the same, although you're essentially aligning sequences in both cases. In mapping, generally speaking, you're alining short nucleotide sequences against a long reference nucleotide sequence. In alignment on the other hand, you generally have a bunch of sequences (nucleotide or protein) that you want to align against each other. There's no master reference sequence that you're aligning against like in mapping. Instead, you're looking for a consensus of sort, e.g. it's not expected that every position matches and gaps, insertions, etc. are not exceptions but the rule. More than that, in alignment, you're generally making use of some kind of substitution matrix such as BLOSUM62. In mapping, the expectation is a 100% match.
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Last edited by rhinoceros; 09-23-2014 at 05:38 AM.
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Old 11-24-2015, 02:06 PM   #14
zyxue
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Quote:
Originally Posted by Felix0902 View Post
What's the differences between alignment, mapping and assembly in Bioinfomatics?
For difference between mapping and alignment, see https://www.broadinstitute.org/files...gen2011_li.pdf
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Old 05-20-2016, 04:38 AM   #15
create.share
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Quote:
Originally Posted by maubp View Post
searching the literature with those keywords for some review papers perhaps?
Your answer was MUCH worst than the question.
Basically this forum could have been MUUUCH much better without your post as it brings nothing; no value only waste reader's time.






Here is the answer:
http://biology.stackexchange.com/que...uence-assembly

Last edited by create.share; 05-20-2016 at 04:44 AM.
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Old 05-23-2016, 03:10 AM   #16
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long answer: https://liorpachter.wordpress.com/20...-read-mapping/
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