User: RT!37

gravatar for RT!37
RT!3720
Reputation:
20
Status:
New User
Location:
India
Last seen:
5 months, 3 weeks ago
Joined:
6 years, 3 months ago
Email:
r***************@gmail.com

Posts by RT!37

<prev • 20 results • page 1 of 2 • next >
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Aligning structurally different parts of distant homologs.
... If there is need to align structurally different parts of distant homologs, which program one should use??. Since, distant homologs often have significant structural changes, that means the assumption of a similar physicochemical environment for aligned residues would be violated?? Any program/to ...
sequence alignment written 5 months ago by RT!3720 • updated 5 months ago by h.mon32k
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scoring matrices computation from transition probability matrix
... The transition probability matrix over time t is computed as P(t) = e ^Qt. In order to calculate a general set of transition probability matrices what type of t values can be used ( t = expected substitutions per site). How these transition probability matrices can be converted to scoring matrice ...
sequence alignment written 2.3 years ago by RT!3720
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Comment: C: Amino Acid matrices freely downloadable url
... Thanks ... !! Similar to BLOSUM and PAM, does we have any resource for VTML series of matrices ?? ...
written 2.4 years ago by RT!3720
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Amino Acid matrices freely downloadable url
... Any resource to d freely download Amino Acid matrices : VTML, OPTIMA, MD, RBLOSUM. Reference articles do not have such urls or it`s not working!! Thanks !! ...
sequence alignment written 2.4 years ago by RT!3720 • updated 2.4 years ago by pevsner420
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Multiple sequence alignment (MSA) of proteins using specific matrix
... I am willing to do MSA for a set of proteins using a specific scoring matrix . There are tools like clustalW, Muscle where one can give a matrix of choice . However, problem is that they switch it later to some other class of matrices and MSA obtained is not the outcome of externally supplied mat ...
alignment written 3.9 years ago by RT!3720
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Benchmark for disordered proteins
... Can Balibase Reference set 9 (linear Motifs) be used as benchmark dataset for disordered proteins ?? ...
sequence alignment written 4.1 years ago by RT!3720
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Gap Opening and Gap Extension penalities in protein alignment
... I have a matrix and want to check its performance. I am stuck at stage of assigning gap penalties (both Gap Opening and Gap Extension). What are the steps involved in getting an optimized gap penalty and is there any web-server which can predict the same ??? ...
alignment written 4.3 years ago by RT!3720
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Comment: C: resource for structural class of proteins
... Thanks Priyabrata !! ...
written 4.4 years ago by RT!3720
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Answer: A: resource for structural class of proteins
... Thanks Priyabrata... Sample: Id retriving Input : A0A4Z3,A0A8M2,A0AT29,A0AT32,A0AT33,A0AV96,A0AVK6,A0AVT1,A0FGR8,A0FGR9,A0FKI7 output pdbs were submitted to Advanced search and Scop Ids mapped Only Output: 2DIS A 131532 [8-103] A0AV96 SCOp Id 131532 : when mapped with parseable file ( ...
written 4.4 years ago by RT!3720
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Comment: C: resource for structural class of proteins
... Thanks genomax2 !!! Example helped me to understand that single Uniprot id can belong to more than 1 class !!! ...
written 4.4 years ago by RT!3720

Latest awards to RT!37

Popular Question 2.3 years ago, created a question with more than 1,000 views. For resource for number of exons and their rank in transcript
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Protein interaction interface prediction from "sequence alone"
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Protein interaction interface prediction from "sequence alone"

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