MAP MUTATION: a program for analyzing mutations in protein sequences

Anwar, Tamanna; Khan, Asad U.

doi:10.6026/97320630001092

Cited by 6 publications

(7 citation statements)

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“…Different domains/motifs were searched at ExPASy server ( http://expasy.org/tools/scanprosite ). Amino acid sequences of both Indian isolates were compared by MAP MUTATION program ( 25 ) to analyze mutations among these isolates.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic Analysis of the Neuraminidase Gene Reveals that the H5N1 Strains Prevalent in Chickens During 2006 Bird Flu Outbreaks in Two Regions of Maharashtra, India are Genetically Different

Danishuddin

Khan

2009

Genomics, Proteomics &Amp; Bioinformatics

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In February 2006, two outbreaks of highly pathogenic avian influenza A virus subtype H5N1 occurred in chickens in two neighboring districts (first in Nandurbar and second in Jalgaon) of Maharashtra, India, in a span of 12 days. In the present study, the neuraminidase (NA) gene of the two Indian H5N1 isolates was taken into consideration to find if the two strains are genetically similar. Phylogenetic analysis of the NA gene showed that the H5N1 strains isolated from the two outbreaks were not originated from the same source. The first Indian isolate (Nandubar/7972/06) was clustered closest to an isolate from chicken in Vietnam in 2004, whereas the second Indian isolate (Jalgaon/8824/06) showed resemblance to strains isolated from swan in Italy and Iran in 2006. Moreover, amino acid sequence analysis showed varying hot spots for substitutions between these two Indian isolates, and three substitutions were found at functional domain sites. Secondary structure changes due to these substitutions were also reported. This study reveals that the H5N1 strains isolated from chickens during 2006 bird flu outbreaks in two neighboring districts of Maharashtra, India are genetically different.

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Section: Methodsmentioning

confidence: 99%

Phylogenetic Analysis of the Neuraminidase Gene Reveals that the H5N1 Strains Prevalent in Chickens During 2006 Bird Flu Outbreaks in Two Regions of Maharashtra, India are Genetically Different

Danishuddin

Khan

2009

Genomics, Proteomics &Amp; Bioinformatics

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“…All mRNAs were gained from the website ( http://www.broad.mit.edu/annotation/ ) and analyzed by CodonW. The averages of G+C, GC3s, Nc, A3s, T3s, G3s and C3s of all genes of the M. grisea genome were computed by Perl program ( 24 ) . Accordingly, the differences between compositions of the putative transferred genes and the average of all genes were determined.…”

Section: Methodsmentioning

confidence: 99%

In silico Analysis of the Potential Infection Mechanisms of Magnaporthe Grisea from Horizontal Gene Transfer Hypothesis

Wang

Peng

et al. 2009

Genomics, Proteomics &Amp; Bioinformatics

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Horizontal gene transfer (HGT) has long been considered as a principal force for an organism to gain novel genes in genome evolution. Homology search, phylogenetic analysis and nucleotide composition analysis are three major objective approaches to arguably determine the occurrence and directionality of HGT. Here, 21 genes that possess the potential to horizontal transfer were acquired from the whole genome of Magnaporthe grisea according to annotation, among which three candidate genes (corresponding protein accession numbers are EAA55123, EAA47200 and EAA52136) were selected for further analysis. According to BLAST homology results, we subsequently conducted phylogenetic analysis of the three candidate HGT genes. Moreover, nucleotide composition analysis was conducted to further validate these HGTs. In addition, the functions of the three candidate genes were searched in COG database. Consequently, we conclude that the gene encoding protein EAA55123 is transferred from Clostridium perfringens. Another HGT event is between EAA52136 and a certain metazoan’s corresponding gene, but the direction remains uncertain. Yet, EAA47200 is not a transferred gene.

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“…The above sequences of the data set were taken to compare with A/Hatay/2004/(H5N1) for the analysis of mutations, using our tool, MAP MUTATION. [ 23 ] Hydrophobicity values were taken out using the tool protscale at expasy server [ 24 ] choosing the Kyte & Doolittle hydrophobicity scale. The secondary structures of the proteins were predicted using secondary structure prediction program, NNPREDICT.…”

Section: Methodsmentioning

confidence: 99%

Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus

Anwar¹,

Khan²

2007

Bioinformation

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Abstract:Influenza virus causes febrile respiratory illness. The infection results in significant mortality, morbidity and economic disruption. In this bioinformatics study, we used the NS1 (the conserved nonstructural) protein of influenza A virus to demonstrate its role in infectivity. Our in silico study revealed a new Casein kinase II (CKII) phosphorylation domain at position 151-154. This domain was formed due to the mutation at position 151 (T151I). Moreover, considerable difference in the secondary structure of this protein due to mutation was also reported. It is also confirmed by contact residue analysis that the changes in secondary structure are due to mutations.

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MAP MUTATION: a program for analyzing mutations in protein sequences

Cited by 6 publications

References 1 publication

Phylogenetic Analysis of the Neuraminidase Gene Reveals that the H5N1 Strains Prevalent in Chickens During 2006 Bird Flu Outbreaks in Two Regions of Maharashtra, India are Genetically Different

Phylogenetic Analysis of the Neuraminidase Gene Reveals that the H5N1 Strains Prevalent in Chickens During 2006 Bird Flu Outbreaks in Two Regions of Maharashtra, India are Genetically Different

In silico Analysis of the Potential Infection Mechanisms of Magnaporthe Grisea from Horizontal Gene Transfer Hypothesis

Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus

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