What's the differences between alignment, mapping and assembly in Bioinfomatics?
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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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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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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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Originally posted by pari_89 View PostHello, 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.
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 informationsavetherhino.org
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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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Originally posted by swbarnes2 View PostIn 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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Originally posted by ahmad87 View PostThis 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!
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
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Originally posted by swbarnes2 View PostThe 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.
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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Originally posted by Jegar View PostThat'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.Last edited by rhinoceros; 09-23-2014, 05:38 AM.savetherhino.org
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Originally posted by maubp View Postsearching the literature with those keywords for some review papers perhaps?
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:
Last edited by create.share; 05-20-2016, 04:44 AM.
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