A computer software package called FasParser has been developed for manipulating sequence data. It can be used on personal computers to perform a series of analyses, including counting and viewing differences between two sequences at both DNA and codon levels, identify overlapping regions between two alignments, sort sequences according to their IDs or lengths, concatenate multiple loci sequences for a particular set of samples, translate DNA to protein, construct alignments with multiple different formats, and also some extraction and filtration analyses on a particular FASTA file. Majority of these functions can be run in a batch mode that is much useful for analyzing large data sets.
An updated version FasParser2 has been released, featuring numerous improvements with sets of novel functions that can facilitate sequence manipulation. Its main additional features include (i) re-designed graphical interface which greatly improves its capability for batch processing, (ii) a trimming function to strip poorly-aligned regions in multiple sequence alignments, (iii) a series of functions that can identify as well as remove 'bad' sequence (either too short or too divergent sequences), (iv) an Editor tool for viewing and editing of biological sequences, and (vi) interfaces (with other programs) for detection of positive selection as well as primer design.
I hope this package will be helpful for a broad audience, particularly those without programming experience in sequence analyses.
Sun Yan-Bo (sunyanbo@mail.kiz.ac.cn)
Kunming Institute of Zoology, Chinese Academy of Sciences
-
The FasParser has been developed into a standalone Windows System Application (compiled and tested on Windows 7/10). It could be run on most Windows systems with no dependence of other programs.
-
Download the latest setup program (i.e. FasParserX.X_setup.exe ) from https://github.com/Sun-Yanbo/FasParser/releases to your disk, and then double click it to install the whole package. It is normally well using the default installation parameters (clicking the Next button).
- Sun Yan-Bo FasParser: A Package for Manipulating Sequence Data. Zoological Research 38(2): 110-112, 2017
- Sun Yan-Bo FasParser2: A Graphical Platform for Batch Manipulation of Tremendous Amount of Sequence Data. Bioinformatics 34(14):2493-2495, 2018