<i>loc</i>BLAST v2.0 - an improved PHP library for embedding standalone NCBI BLAST+ program to an interactive graphical user interface

Kumar, T. Ashok

doi:10.1101/556225

2019

DOI: 10.1101/556225

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locBLAST v2.0 - an improved PHP library for embedding standalone NCBI BLAST+ program to an interactive graphical user interface

T. Ashok Kumar

Abstract: Background: NCBI BLAST is a most popularly used sequence analysis platform in a broad range of applications. The final release of standalone WWW BLAST server (wwwBLAST v2.2.26) of NCBI was officially released on May 10, 2004, and discontinued its support. Due to the popularity and high demand, the BLAST algorithms were refined with rich features and released as online BLAST, standalone BLAST+, BLAST RESTful service, and cloud BLAST server. locBLAST v2.0 is a lightweight PHP library, designed in preference to W… Show more

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Cited by 2 publications

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AniAMPpred: artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom

Sharma

Shrivastava

Singh

et al. 2021

Briefings in Bioinformatics

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With advancements in genomics, there has been substantial reduction in the cost and time of genome sequencing and has resulted in lot of data in genome databases. Antimicrobial host defense proteins provide protection against invading microbes. But confirming the antimicrobial function of host proteins by wet-lab experiments is expensive and time consuming. Therefore, there is a need to develop an in silico tool to identify the antimicrobial function of proteins. In the current study, we developed a model AniAMPpred by considering all the available antimicrobial peptides (AMPs) of length $\in $[10 200] from the animal kingdom. The model utilizes a support vector machine algorithm with deep learning-based features and identifies probable antimicrobial proteins (PAPs) in the genome of animals. The results show that our proposed model outperforms other state-of-the-art classifiers, has very high confidence in its predictions, is not biased and can classify both AMPs and non-AMPs for a diverse peptide length with high accuracy. By utilizing AniAMPpred, we identified 436 PAPs in the genome of Helobdella robusta. To further confirm the functional activity of PAPs, we performed BLAST analysis against known AMPs. On detailed analysis of five selected PAPs, we could observe their similarity with antimicrobial proteins of several animal species. Thus, our proposed model can help the researchers identify PAPs in the genome of animals and provide insight into the functional identity of different proteins. An online prediction server is also developed based on the proposed approach, which is freely accessible at https://aniamppred.anvil.app/.

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AniAMPpred: artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom

Sharma

Shrivastava

Singh

et al. 2021

Briefings in Bioinformatics

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ProtPathDB: A Web-based Resource of Parasite Proteases

Shehzad

Pandey

Sharma

et al. 2022

CBIO

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Proteases regulate cell proliferation, cell growth, biological processes, and overall homeostasis. Several proteases are extensively annotated and well-characterized in pathogenic organisms such as bacteria, parasites, and microbial species as anti-bacterial, anti-parasitic and anti-microbial. Several of these proteins are being explored as viable targets for various drug discovery research in various microbial diseases. Despite multiple studies on pathogen proteases, the comprehensive information on pathogen proteases is scattered or redundant, if available. We have developed a comprehensive and integrative protease database resource, ProtPathDB, for 23 pathogen species distributed among five taxa, Amoebozoa, Apicomplexa, Heteroloblosea, Kinetoplastida and Fungi. ProtPathDB collects and organizes sequences, class division, signal peptides, localization, post-translational modifications, three-dimensional structure and related structural information regarding binding sites, and binding scores of annotated proteases. The ProtPathDB is publicly available at http://bioinfo.icgeb.res.in/ProtPathDB. We believe that the database will be a one-stop resource for integrative and comparative analysis of pathogen proteases to better understand the functions of the microbial proteases and help drug discovery efforts target proteases.

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locBLAST v2.0 - an improved PHP library for embedding standalone NCBI BLAST+ program to an interactive graphical user interface

Cited by 2 publications

References 6 publications

AniAMPpred: artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom

AniAMPpred: artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom

ProtPathDB: A Web-based Resource of Parasite Proteases

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