HIVTools (NGlyAlign) #################################
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This is the main code folder. It contains the following files:
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example_NGlyAlignRun.m to execute NGlyAlign with the input fasta file.
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main_NGlyAlign.m is the main function that takes sequence as fasta format. It allows either of the following options
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option 1(default): main_NGlyAlign(inFile) Input fasta file must be aligned as a requirement to compute global scores, conserved anchors and block anchors.
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option 2: main_NGlyAlign(inFile,'anchorSelect','single'); a) Input can be aligned or ungapped/unaligned fasta file b) The parameter 'anchorSelect' is set to value 'single' to specify program to generate only glycosylation block anchors (global scores and conserved anchors are not generated).
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option 3:main_NGlyAlign(inFile,'anchorSelect','all','setGlobal','true','scoringMatrix',x,'cutoff',y) a) Input fasta file must be aligned. b) 'anchorSelect' is set 'all' c) 'setGlobal' is set 'true' d) 'scoringMatrix' is set to value x where x is the selection of the scoring matrix 'identity' or 'blosum' e) 'cutoff' is set to threshold y, starting from 95 to 100 (when x is set to use 'identity' matrix) or 0 to 0.85 (when x is set to use 'blosum' scoring matrix with entropy)
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function_generateConservedAnchors.m contains required functions to compute global scores and generate conserved anchors
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function_consensusByIdentity.m contains function to compute percentage of identical residue appeared at each position in MSA.
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function_generateGBlockAnchors.m contains required functions to identify glycosylation motifs and their positions to generate block anchors.
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contains test file Ref_Kerkhof92_aligned_V1.fasta (collected from van den Kerkhof TLGM, Feenstra K, Euler Z, van Gils MJ, Rijsdijk LWE, Boeser-Nunnink BD, et al. HIV-1 envelope glycoprotein signatures that correlate with the development of cross-reactive neutralizing activity. Retrovirology. 2013;10:102. doi:10.1186/1742-4690-10-102.)
The output contains
- globalScores.txt global scores (percentage identity or entropy) for each alignment position in MSA.
- glycosylationPositions.txt List of glycosylation indices for each strain in ungapped alignment MSA.
- NGlyAnchors.txt List of anchors to use as an input for Dialign2.
Final step to align variable region requires -NGlyAnchors.txt -input fasta file with two options to run Dialign a) use online version http://dialign.gobics.de/anchor/submission.php b) Download latest version of Dialign (C++) from (http://dialign.gobics.de/)