Tag: Sequence Similarity

PyMod 1.1 – Sequence Similarity Searches, Multiple Sequence-structure Alignments, and Homology Modelling within PyMOL

PyMod 1.1

:: DESCRIPTION

A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., BLAST, ClustalW, Muscle, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modelling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks.PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures.

::DEVELOPER

PyMod team

:: SCREENSHOTS

PyMod

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Python
  • PyMol
  • BioPython
  • Numpy, BLAST+ 2.2.25+, MUSCLE, ClustalW and MODELLER

:: DOWNLOAD

   PyMod

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S2. doi: 10.1186/1471-2105-13-S4-S2.
PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL.

PFP / ESG – Sequence Similarity-based Protein Function Prediction server

PFP / ESG

:: DESCRIPTION

PFP (Protein Function Prediction) is a sequence similarity-based protein function prediction server designed to predict GO annotations for a query sequence beyond what can be found by conventional database search such as BLAST.It takes into account weakly similar sequences as well as GO term associations observed in known annotations.

ESG (Extended Similarity Group) is a sequence similarity-based protein function prediction server. It employ PSI-BLAST iteratively and essentially selects GO term annotations that appear consistently in the searches.

Combined PFP & ESG interface.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PFP/ESG: Automated protein function prediction servers enhanced with Gene Ontology visualization tool.
Khan IK, Wei Q, Chitale M, Kihara D.
Bioinformatics. 2015 Jan 15;31(2):271-2. doi: 10.1093/bioinformatics/btu646.

GHOST-MP 1.3.4 – Parallel Sequence Similarity Search Tool

GHOST-MP 1.3.4

:: DESCRIPTION

GHOST-MP is a parallel sequence similarity search tool. It searches for similar sequences among nucleotide query sequences and amino acid sequence database like BLASTX.

::DEVELOPER

Akiyama Laboratory , Tokyo Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

GHOST-MP

:: MORE INFORMATION

Citation

Int J Mol Sci. 2017 Oct 11;18(10). pii: E2124. doi: 10.3390/ijms18102124.
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data.
Kakuta M, Suzuki S, Izawa K, Ishida T, Akiyama Y

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