IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments

被引：8

作者：

Pervez, Muhammad Tariq ^{[1
,2
]}

Babar, Masroor Ellahi ^{[3
]}

Nadeem, Asif ^{[2
]}

Aslam, Naeem ^{[2
,4
]}

Naveed, Nasir ^{[5
]}

Ahmad, Sarfraz ^{[1
]}

Muhammad, Shah ^{[1
]}

Qadri, Salman ^{[6
]}

Shahid, Muhammad ^{[7
]}

Hussain, Tanveer ^{[3
]}

Javed, Maryam ^{[2
]}

机构：

[1] Virtual Univ Pakistan, Dept Comp Sci, Lahore, Pakistan

[2] Univ Vet & Anim Sci, Inst Biochem & Biotechnol, Lahore, Pakistan

[3] Virtual Univ Pakistan, Dept Bioinformat, Lahore, Pakistan

[4] NFC Inst Engn & Technol, Dept Comp Sci, Multan, Pakistan

[5] Univ Koblenz Landau, Inst Web Sci & Technol, Landau, Germany

[6] Islamia Univ Bahawalpur, Dept Comp Sci, Bahawalpur, Pakistan

[7] SE Coll Bahawalpur, Govt Sadiq Egerton Coll Bahawalpur, Dept Phys, Bahawalpur, Pakistan

来源：

EVOLUTIONARY BIOINFORMATICS | 2015年 / 11卷

关键词：

MSA editing tool; MSA comparator; FASTA; MSA Identity Matrix;

D O I：

10.4137/EBO.S18980

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：35 / 42

页数：8

共 50 条

[1] SeqTools: Visual tools for manual analysis of sequence alignments
Barson G.
Griffiths E.
BMC Research Notes, 9 (1)
[2] FINGERPRINT: visual depiction of variation in multiple sequence alignments
Lou, Melanie
Golding, G. Brian
MOLECULAR ECOLOGY NOTES, 2007, 7 (06): : 908 - 914
[3] MSAViewer: interactive Java']JavaScript visualization of multiple sequence alignments
Yachdav, Guy
Wilzbach, Sebastian
Rauscher, Benedikt
Sheridan, Robert
Sillitoe, Ian
Procter, James
Lewis, Suzanna E.
Rost, Burkhard
Goldberg, Tatyana
BIOINFORMATICS, 2016, 32 (22) : 3501 - 3503
[4] Multiple sequence alignments as tools for protein structure and function prediction
Valencia, A
COMPARATIVE AND FUNCTIONAL GENOMICS, 2003, 4 (04): : 424 - 427
[5] Exploratory visual analysis of conserved domains on multiple sequence alignments
TJ Jankun-Kelly
Andrew D Lindeman
Susan M Bridges
BMC Bioinformatics, 10
[6] Phylo-VISTA: interactive visualization of multiple DNA sequence alignments
Shah, N
Couronne, O
Pennacchio, LA
Brudno, M
Batzoglou, S
Bethel, EW
Rubin, EM
Hamann, B
Dubchak, I
BIOINFORMATICS, 2004, 20 (05) : 636 - U122
[7] Exploratory visual analysis of conserved domains on multiple sequence alignments
Jankun-Kelly, T. J.
Lindeman, Andrew D.
Bridges, Susan M.
BMC BIOINFORMATICS, 2009, 10 : S7
[8] Exploratory visual analysis of conserved domains on multiple sequence alignments
Jankun-Kelly, T.J.
Lindeman, Andrew D.
Bridges, Susan M.
BMC Bioinformatics, 2009, 10 (SUPPL. 11):
[9] Multiple sequence alignments
Wallace, IM
Blackshields, G
Higgins, DG
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2005, 15 (03) : 261 - 266
[10] Alignment Cubes: Towards Interactive Visual Exploration and Evaluation of Multiple Ontology Alignments
Ivanova, Valentina
Bach, Benjamin
Pietriga, Emmanuel
Lambrix, Patrick
SEMANTIC WEB - ISWC 2017, PT I, 2017, 10587 : 400 - 417

← 1 2 3 4 5 →