Rahel is a lytic Myoviridae bacteriophage that infects Mycobacterium smegmatis mc2155. It has 1,555,955 bp and 64.7% G+C content. Rahel has a circularly permuted genome with 270 genes, 53 of them of known function, 33 tRNAs, and 1 transfer-messenger RNA (tmRNA). Only five genes are coded on the reverse strand.
NCBI BLAST is a most popular bioinformatics framework for finding local similarity between two or more biological sequences. It provides integrative access to various biological databases through web user interface, commandline user interface, and application programming interface. BLASTphp is a lightweight PHP library that wrap's NCBI BLAST's RESTful API into a custom graphical user interface BLAST. The BLASTphp program remotely executes the NCBI BLAST through the HTTP/HTTPS interface and elicits the response in HTML, XML, XML2, JSON2, Text, or Tabular (plain) format. However, it can be easily connected to a webserver and integrated with any SQL database which contain the biological sequences. BLASTphp is freely available under GNU General Public License version 3 (GPLv3), at https://github.com/AshokHub/BLASTphp.
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 WWW BLAST server. It masks command-line BLAST+ programs to a rich graphical user interface (GUI).
Methods:The locBLAST v2.0 library was designed using PHP, CSS, pure JavaScript, and standalone NCBI BLAST+ executables.Results: locBLAST v2.0 provides an interactive web interface to input query sequences through the web form and provides a graphical report of the sequence alignment result. The graphical overview, tabular summary, and formatted sequence alignment of locBLAST v2.0 result mimic to the native format of online NCBI BLAST result. It allows users to perform both local and online database search.Availability: Freely available at https://github.com/AshokHub/locBLAST
Background: Protein Data Bank (PDB) is the most popular structure database that contains experimentally determined three-dimensional (3D) structures of biological macromolecules and small molecules. The rich features of PDB are keyword assisted advanced text search, structure search by sequence alignment, sequence motif search, ligand to target-ligand complex search through SMILES substructure search, JSON API query search, structure alignment, structure quality assessment, genome viewer, and 3D structure viewer. It is widely used in molecular modelling and computer-aided drug design. PDB cle is a simple tool to extract chain sequence of protein/nucleotide and 3D structure of protein/ nucleotide/ ligand from the PDB. Objectives: To construct an online tool for separating molecule-wise chain sequence and structure of polymers and non-polymer structures in a macromolecule. Moreover, the separated sequences and structures are produced to moleculespecific standard file format. Methods: The graphical web-interface of PDB cle tool has been designed using PHP, CSS, and pure JavaScript. Parsing the atomic coordinate records and sequence records from the PDBML/XML file and/or PDBx/mmJSON file through the API of PDB was done through PHP server script. Findings: The PDB cle tool retrieves and generates separate structure/sequence files for each amino acid/RNA chain, and pair of chains for DNA base pairs with/without ligand complex from the PDB. The ligand molecules are separated and sorted from the chains and produced to an SDF file. Applications: PDB cle tool is publicly accessible at https://www.biogem.org/tool/pdbcle/.
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