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IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

Pervez MT, Babar ME, Nadeem A, Aslam N, Naveed N, Ahmad S, Muhammad S, Qadri S, Shahid M, Hussain T, Javed M - Evol. Bioinform. Online (2015)

Bottom Line: MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively.MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds.Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan. ; Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.

ABSTRACT
IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

No MeSH data available.


Main interface of IVisTMSA. This provides links to start the seven tools of IVisTMSA. The specific tool can be run by clicking the respective link.
© Copyright Policy - open-access
Related In: Results  -  Collection


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f1-ebo-11-2015-035: Main interface of IVisTMSA. This provides links to start the seven tools of IVisTMSA. The specific tool can be run by clicking the respective link.

Mentions: All tools of IVisTMSA (Fig. 1) are written in Java programming language. NetBeans IDE (Integrative Development Environment) 7.4 was used to write IVisTMSA. XML was used for saving the state of the work performed in MSApad and MSA comparator. BioJava was used to embed Jmol in IVisTMSA. A computing machine having Core i7 3.34-GHz processor and 8-GB RAM was used to write and analyze IVisTMSA.


IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

Pervez MT, Babar ME, Nadeem A, Aslam N, Naveed N, Ahmad S, Muhammad S, Qadri S, Shahid M, Hussain T, Javed M - Evol. Bioinform. Online (2015)

Main interface of IVisTMSA. This provides links to start the seven tools of IVisTMSA. The specific tool can be run by clicking the respective link.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4362671&req=5

f1-ebo-11-2015-035: Main interface of IVisTMSA. This provides links to start the seven tools of IVisTMSA. The specific tool can be run by clicking the respective link.
Mentions: All tools of IVisTMSA (Fig. 1) are written in Java programming language. NetBeans IDE (Integrative Development Environment) 7.4 was used to write IVisTMSA. XML was used for saving the state of the work performed in MSApad and MSA comparator. BioJava was used to embed Jmol in IVisTMSA. A computing machine having Core i7 3.34-GHz processor and 8-GB RAM was used to write and analyze IVisTMSA.

Bottom Line: MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively.MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds.Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan. ; Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.

ABSTRACT
IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

No MeSH data available.