Volume 38 Issue 2
Mar.  2017
Turn off MathJax
Article Contents

Yan-Bo Sun. FasParser: a package for manipulating sequence data. Zoological Research, 2017, 38(2): 110-112. doi: 10.24272/j.issn.2095-8137.2017.017
Citation: Yan-Bo Sun. FasParser: a package for manipulating sequence data. Zoological Research, 2017, 38(2): 110-112. doi: 10.24272/j.issn.2095-8137.2017.017

FasParser: a package for manipulating sequence data

doi: 10.24272/j.issn.2095-8137.2017.017
Funds:  The development of this package was promoted by the data accumulated through the programs of the National Natural Science Foundation of China (31671326, 81602346, and 31401958)
More Information
  • Corresponding author: Yan-Bo Sun
  • Received Date: 2017-02-01
  • Rev Recd Date: 2017-03-01
  • Publish Date: 2017-03-18
  • A computer software package called ‘FasParser’ was developed for manipulating sequence data. It can be used on personal computers to perform series of analyses, including counting and viewing differences between two sequences at both DNA and codon levels, identifying overlapping regions between two alignments, sorting of sequences according to their IDs or lengths, concatenating sequences of multiple loci for a particular set of samples, translating nucleotide sequences to amino acids, and constructing alignments in several different formats, as well as some extracting and filtrating of data for a particular FASTA file. Majority of these functions can be run in a batch mode, which is very useful for analyzing large data sets. This package can be used by a broad audience, and is designed for researchers that do not have programming experience in sequence analyses. The GUI version of FasParser can be downloaded from https://github.com/Sun-Yanbo/FasParser, free of charge.
  • 加载中
  • [1] Edgar RC. 2004. MUSCLE:a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5:113.
    [2] Hall TA. 1999. BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41:95-98.
    [3] Jordan G, Goldman N. 2012. The effects of alignment error and alignment filtering on the sitewise detection of positive selection. Molecular Biology and Evolution, 29(4):1125-1139.
    [4] Katoh K, Misawa K, Kuma KI, Miyata T. 2002. MAFFT:a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14):3059-3066.
    [5] Kumar S, Tamura K, Nei M. 1994. MEGA:molecular evolutionary genetics analysis software for microcomputers. Computer Applications in Biosciences, 10(2):189-191.
    [6] Liu J, Wang LD, Sun YB, Li EM, Xu LY, Zhang YP, Yao YG, Kong QP. 2012. Deciphering the signature of selective constraints on cancerous mitochondrial genome. Molecular Biology and Evolution, 29(4):1255-1261.
    [7] Löytynoja A, Goldman N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences of the United States of America, 102(30):10557-10562.
    [8] Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution, 3(5):418-426.
  • 加载中
通讯作者: 陈斌, bchen63@163.com
  • 1. 

    沈阳化工大学材料科学与工程学院 沈阳 110142

  1. 本站搜索
  2. 百度学术搜索
  3. 万方数据库搜索
  4. CNKI搜索

Article Metrics

Article views(1135) PDF downloads(1395) Cited by()

Related
Proportional views

FasParser: a package for manipulating sequence data

doi: 10.24272/j.issn.2095-8137.2017.017
Funds:  The development of this package was promoted by the data accumulated through the programs of the National Natural Science Foundation of China (31671326, 81602346, and 31401958)
    Corresponding author: Yan-Bo Sun

Abstract: A computer software package called ‘FasParser’ was developed for manipulating sequence data. It can be used on personal computers to perform series of analyses, including counting and viewing differences between two sequences at both DNA and codon levels, identifying overlapping regions between two alignments, sorting of sequences according to their IDs or lengths, concatenating sequences of multiple loci for a particular set of samples, translating nucleotide sequences to amino acids, and constructing alignments in several different formats, as well as some extracting and filtrating of data for a particular FASTA file. Majority of these functions can be run in a batch mode, which is very useful for analyzing large data sets. This package can be used by a broad audience, and is designed for researchers that do not have programming experience in sequence analyses. The GUI version of FasParser can be downloaded from https://github.com/Sun-Yanbo/FasParser, free of charge.

Yan-Bo Sun. FasParser: a package for manipulating sequence data. Zoological Research, 2017, 38(2): 110-112. doi: 10.24272/j.issn.2095-8137.2017.017
Citation: Yan-Bo Sun. FasParser: a package for manipulating sequence data. Zoological Research, 2017, 38(2): 110-112. doi: 10.24272/j.issn.2095-8137.2017.017
Reference (8)

Catalog

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return