Questions tagged [sequence-analysis]

Analysis of DNA, RNA or protein (amino acid) sequences. Here sequences are compared so analyze similarities and conserved regions. Sequence analysis is usually done by specialized software.

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What is the difference between local and global sequence alignments?

There are a bunch of different alignment tools out there, and I don't want to get bogged down in the maths behind them as this not only between software but varies from software version to version. ...
James's user avatar
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11 votes
1 answer
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Sequence evolution simulation tool

I'm looking for a tool to simulate sequence evolution given a specific mutation model and birth-death model. I'm aware of tools and packages like INDELible, Seq-Gen and PhyloSim, but they simulate ...
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5 votes
3 answers
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What is the state-of-the-art algorithm for multiple sequence alignment?

Which algorithm or algorithms are considered the standard or state-of-the-art for multiple sequence alignment? How big is the need for better algorithms? How many sequences need to be alignment in a ...
msa's user avatar
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3 votes
1 answer
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What are Codominant vs Dominant Genetic Markers?

When talking about types of genetic markers, the adjective "dominant" and "codominant" are often used. I don't fully understand their definitions and found contradicting definitions. Foll and ...
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7 votes
2 answers
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Comparative evolutionary study: is amino acid or nucleotide comparison more useful?

I am a high school student and am currently learning about evolutionary relationship study in biology. My teacher said that a comparative study of amino acid sequences is more useful than a ...
Szeto's user avatar
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5 votes
1 answer
2k views

How to do multiple sequence alignment?

I have a DNA sequence that makes protein 1. but now I have asked to: compare the amino acid sequence of protein 1 with nine homologous proteins and make a multi sequence alignment (MSA) of the ...
Nhung Pham's user avatar
3 votes
0 answers
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Good poly-A filtering rules or tools

I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have ...
highBandWidth's user avatar
3 votes
1 answer
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Why is Cysteine and Tyrosine used to calculate a sequence isoelectric point?

Why are the amino acids - cysteine and tyrosine used in isoelectric point calculations for a protein sequence, yet neither of them are positively charged molecules? and are not used in net charge ...
user2679447's user avatar
1 vote
1 answer
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What is the difference between 4th generation sequencing and NGS?

The generation of sequencing technologies has come on leaps and bounds and there are stark differences between the types of technology used. There is a great Q&A here What is the difference ...
James's user avatar
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