BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA, and protein sequences at sequence level and residue level based on machine learning approaches

Version-1.0 created on 2019-04-12

BioSeq-Analysis2.0.rar -- The source rar file for stand-alone package on Windows, Linux, Unix.

Quick to start

BioSeq-Analysis2.0_manual.pdf for how to use stand-alone program of BioSeq-Analysis2.0.

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Version-1.1 created on 2019-11-22

New Version stand-alone tools release notes

1.Since Python 2.7 will not be maintained past 2020, this time we launched two BioSeq-Analysis2.0
stand-alone packages supporting Python 3.6 and Python 2.7 respectively.
2.Solve the problem of using FlexCRFs-0.3 on Windows system by deploying Linux virtual environment.
3.Solve the connection problem on Windows when parent process coordinates a set of its children process.
4.Add external software for Secondary structure feature extraction method for RNA sequences in Res part.
5.Fix the bug coming from internal test and users feedback.
6.Modify the manual and add more details.

BioSeq-Analysis2.0_py2.rar -- The source rar file for stand-alone package on Windows, Linux, Unix.

BioSeq-Analysis2.0_py3.rar -- The source rar file for stand-alone package on Windows, Linux, Unix.

Quick to start

BioSeq-Analysis2.0_py2&py3-manual.pdf for how to use stand-al

Supporting Information for the physicochemical indices

Supporting Information S1-DNA-90.txt
-- The 90 physicochemical indices for dinucleotides(DNA) used in BioSeq-Analysis2.0(1-2).

Supporting Information S2-DNA-12.xls
-- The 12 physicochemical indices for trinucleotides(DNA) used in BioSeq-Analysis2.0(1).

Supporting Information S3-RNA-11.txt
-- The 11 physicochemical indices for dinucleotides(RNA) used in BioSeq-Analysis2.0(1).

Supporting Information S4-aaindex.txt
-- The 547 physicochemical indices for amino acids used in BioSeq-Analysis2.0(3).

References:

1.Chen, W., Zhang, X.T., Brooker, J., Lin, H., Zhang, L.Q. and Chou, K.C. (2015) PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions.Bioinformatics, 31, 119.
2.Friedel, M., Nikolajewa, S., Suhnel, J. and Wilhelm, T. (2009) DiProDB: a database for dinucleotide properties. Nucleic Acids Research, 37, D37-D40.
3.Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T. and Kanehisa, M. (2008) AAindex: amino acid index database, progress report 2008.Nucleic Acids Research, 36,D202-D205.