User: mithrandir

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mithrandir40
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New User
Location:
India
Last seen:
1 year, 7 months ago
Joined:
2 years, 5 months ago
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Posts by mithrandir

<prev • 7 results • page 1 of 1 • next >
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What does '*' Amino Acid in BLOSUM Matrix of MATLAB mean?
... The BLOSUM(n) [e.g. BLOSUM(62)] returns a 24 by 24 matrix with the following amino acid sequence 'A R N D C Q E G H I L K M F P S T W Y V B Z X *'. The first 20 are amino acids, the next three are special amino acid characters, what does * stand for? Does it stand for Gap(-). Source: http://in.mathw ...
amino acid blosum protein matlab written 19 months ago by mithrandir40 • updated 19 months ago by Michael Dondrup43k
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Comment: C: How to score a multiple sequence alignment (MSA)?
... Hi Anand. I do not have a reference alignment(have updated the question) hence I cannot use Edgar's qscore.  ...
written 23 months ago by mithrandir40
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How to score a multiple sequence alignment (MSA)?
... I want to compare two MSAs of the same set of protein sequences and determine which is better(I do not have the 'true alignment'). One way is the sum of pairs method. But I think sum of pairs is defined for a column in an alignment(average of scores of all pairs of residues). So, how do we calculate ...
sequence alignment protein msa written 23 months ago by mithrandir40 • updated 4 days ago by hmnipunad0
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Is there a server for Multiple Sequence alignment using POA( Partial Order Alignment) that uses the partial order graph algorithm?
... Is there a server over which we can submit a set of sequences and get an alignment that uses partial order graph algorithm for multiple sequence alignment? I found one server but it looks it has been moved -http://www.bioinformatics.ucla.edu/poa ...
alignment sequence protein msa poa written 23 months ago by mithrandir40 • updated 23 months ago by Biostar ♦♦ 20
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What do the scores in a BLOSUM matrix mean?
... For example in BLOSUM62 Matrix there are negative scores for some pairs and zero for some, what does it mean by having a negative or zero score here? I suppose the more the score the more similar the amino acids are. Am I right in saying this? BLOSUM62 Matrix here https://upload.wikimedia.org/wiki ...
score blosum sequence protein alignment written 23 months ago by mithrandir40 • updated 23 months ago by Jean-Karim Heriche13k
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How to know the accuracy of a Multiple Sequence Alignment?
... I have a set of protein sequences which I have aligned by using different Multiple Sequence Alignment methods such as TM-Coffee, MUSCLE, multialign in MATLAB, etc. Since this set of sequences is very divergent the alignment I am getting from different tools is very different so I am searching for a ...
sequence alignment protein msa written 23 months ago by mithrandir40 • updated 23 months ago by Jean-Karim Heriche13k
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Is there a Transmembrane Topology Prediction tool in which one can specify the number of Transmembrane domains to be found ?
... I want to find the Transmembrane domains in a sequence of protein. The number of transmembrane domains displayed by various tools differs. I have used TOPCONS, OCTOPUS, etc. Is there a tool in which I can force the output to give the desired number of transmembrane domains? ...
software bioinformatics protein tool transmembrane written 23 months ago by mithrandir40 • updated 23 months ago by Michael Dondrup43k

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