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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4
votes
2answers
178 views

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 ...
5
votes
1answer
134 views

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 ...
3
votes
1answer
310 views

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 ...
3
votes
0answers
129 views

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 ...