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Sequence Analysis

Sequence search against a set of local sequences (local database) using phmmer

in Proteomics/Sequence Analysis/Softwares by

PHMMER is a sequence analysis tool used for protein sequences (http://hmmer.org; version 3.1 b2). It is available online as a web server and as well as a part of the HMMER stand-alone package (http://hmmer.org; version 3.1 b2). HMMER offers various useful features such as multiple sequence alignment including the file format conversion.  Continue reading “Sequence search against a set of local sequences (local database) using phmmer” »

Biotite: A bioinformatics framework for sequence and structure data analysis

in Sequence Analysis/Softwares/Structural Bioinformatics by

Sequence and structural data in bioinformatics are ever-increasing and the need for its analysis is ever-demanding likewise. As bioinformaticians analyze the data with their keen knowledge and reach important conclusions, similarly, bioinformaticists provide with the enhanced and advanced tools and software for data analysis. Continue reading “Biotite: A bioinformatics framework for sequence and structure data analysis” »

Simulated sequence alignment software: An alternative to MSA benchmarks

in Algorithms/Databases/Sequence Analysis/Softwares/Tools by

In our previous article, we discussed different multiple sequence alignment (MSA) benchmarks to compare and assess the available MSA programs. However, since the last decade, several sequence simulation software have been introduced and are gaining more interest. In this article, we will be discussing various sequence simulating software being used as alternatives to MSA benchmarks. Continue reading “Simulated sequence alignment software: An alternative to MSA benchmarks” »

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