BSSB: BLAST Server for Structural Biologists

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processing BLAST output, but...

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Published inJournal of applied crystallography Vol. 44; no. 3; pp. 651 - 654
Main Authors Uthayakumar, Muthukumarasamy, Sowmiya, Govindhan, Sabarinathan, Radhakrishnan, Udayaprakash, N., Kirti Vaishnavi, M., Sekar, Kanagaraj
Format Journal Article
LanguageEnglish
Published 5 Abbey Square, Chester, Cheshire CH1 2HU, England International Union of Crystallography 01.06.2011
Blackwell Publishing Ltd
Subjects
Alignment
Biologists
BLAST
BSSB
Crystal structure
Crystallography
Decisions
Molecular biology
Molecular structure
Nucleic acids
protein crystallography
Proteins
Searching
sequence alignment
Servers
Software
structure visualization
Online AccessGet full text
ISSN1600-5767
0021-8898
1600-5767
DOI10.1107/S0021889811008387

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Summary:The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processing BLAST output, but none of them provide three‐dimensional structure visualization. This shortcoming has been addressed in the proposed tool BLAST Server for Structural Biologists (BSSB), which maps a BLAST output onto the three‐dimensional structure of the subject protein. The three‐dimensional structure of the subject protein is represented using a three‐color coding scheme (identical: red; similar: yellow; and mismatch: white) based on the pairwise alignment obtained. Thus, the user will be able to visualize a possible three‐dimensional structure for the query protein sequence. This information can be used to gain a deeper insight into the sequence–structure correlation. Furthermore, the additional structure‐level information enables the user to make coherent and logical decisions regarding the type of input model structure or fragment that can be used for molecular replacement calculations. This tool is freely available to all users at http://bioserver1.physics.iisc.ernet.in/bssb/.
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ISSN:1600-5767
0021-8898
1600-5767
DOI:10.1107/S0021889811008387