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Oct
16
comment Do the bacterial species X, Y, Z code for proteins A, B, C?
@codax no, each query protein should have its own set of HSPs. You are looking for HSPs that have i) high sequence identity and ii) cover the entire length of the query sequence (or nearly). Now that you know they are there and have high similarity, you can also use exonerate to match the genes more precisely.
Oct
13
comment Applications of shortest path problem
@TanMath here you go, but it won't help you much. The shortest path analysis was a tiny part of the work, I only mentioned it because I happened to have done this recently. Your best bet is to go on PubMed and search for "shortest path".
Oct
13
revised Applications of shortest path problem
added 158 characters in body
Oct
13
answered Applications of shortest path problem
Oct
9
comment Why do my 23andme results only show me as 8.2% Scandinavian?
@Amory actually, I would guess that's not true, strictly speaking. I doubt that chromosomal cross-over would produce a 50% split. I would expect a range of 49.999-50.0001% or so from each parent. If we're being pedantic, that is :)
Oct
6
comment Do the bacterial species X, Y, Z code for proteins A, B, C?
@codax OK, if you have a list of proteins you want, get their sequences from a related species of bacterium, the closer the better, and use those sequences to query your target genomes. The methods I describe are sensitive enough to deal with small differences in sequence.
Oct
5
revised Can the RNA in the HIV virus make viral enzymes without entering the nucleus?
added 1 character in body
Oct
4
comment Do the bacterial species X, Y, Z code for proteins A, B, C?
@codax that's a completely different question! What are you trying to do? WHat do you have and what are you looking for? Don't you have a list of proteins in species X and want to find them in species Y?
Oct
4
comment Effect of a doubling of the start codon in a gene
Very good answer and +1. Just a nitpick: strictly speaking, there are actually tRNAs that recognize STOP codons. Such nonsense tRNAs can be the product of a specific mutation but also, as is the case for tRNASec, wild type sequences that insert a specific amino acid.
Oct
4
comment Effect of a doubling of the start codon in a gene
If one of these answers solved your issue, please take a moment and accept it by clicking on the check mark to the left. That will mark the question as answered and is the way thanks are expressed on the Stack Exchange sites.
Oct
4
revised Meaning of “pure” in “pure plant DNA” (horizontally transferred to bacteria in soil conditions)
edited title
Oct
3
comment Are there examples of animals that adapt to their environment very quickly? The phenomenon is called Phenoptic Plasticity
First of all, that also happens with all animals. If you have enough food, you grow big, if you don't you remain small. Please edit your question and clarify.
Oct
3
reviewed Approve Why are there no known animals with an odd number of legs?
Oct
3
comment Are there examples of animals that adapt to their environment very quickly? The phenomenon is called Phenoptic Plasticity
What do you mean? All of them do. Every single one.
Oct
2
revised Do the bacterial species X, Y, Z code for proteins A, B, C?
added 6 characters in body
Oct
1
comment Do the bacterial species X, Y, Z code for proteins A, B, C?
I think the OP needs to identify genes in the genomic sequence and only has proteins from one species. Multiple alignment won't help.
Oct
1
answered Do the bacterial species X, Y, Z code for proteins A, B, C?
Oct
1
reviewed Leave Open Why do we urinate more when we are nervous?
Oct
1
reviewed Close Can anyone please help me identify this plant?
Oct
1
comment Can anyone please help me identify this plant?
Thanks for the edit, but please answer all 5 questions that AliceD asked.