Acta Scientific Microbiology (ASMI) (ISSN: 2581-3226)

Short Communication Volume 3 Issue 6

SeqProperties: A Python Command-Line Tool for Basic Sequence Analysis

Maurice HT Ling

Colossus Technologies LLP, Singapore, HOHY PTE LTD, Singapore

*Corresponding Author: Maurice HT Ling, Colossus Technologies LLP, Singapore, HOHY PTE LTD, Singapore.

Received: April 27, 2020; Published: May 20, 2020

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Abstract

  Command-line tools are the fundamental building blocks of main bioinformatics applications [1,2]. Despite a burden to noncomputer affine biologists [3], command-line tools can serve as underlying operations for chaining into analysis pipelines [4-10] or for integration into applications with graphical user interfaces.

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References

  1. S Liu and Z Liu. “Introduction to Linux and command line tools for bioinformatics”. In Bioinformatics in Aquaculture, Z. J. Liu, Ed. Chichester, UK: John Wiley and Sons, Ltd (2017): 1-29.
  2. T Seemann. “Ten recommendations for creating usable bioinformatics command line software”. Gigascience 1 (2013): 15.
  3. DK Morais., et al. “BTW - Bioinformatics through Windows: an easy-to-install package to analyze marker gene data”. Peer Journal 6 (2018): e5299.
  4. SP Sadedin., et al. “Bpipe: a tool for running and managing bioinformatics pipelines”. Bioinformatics11 (2012): 1525-1526.
  5. A Zhou., et al. “PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool”. Bioinformatics9 (2018): 1603-1605.
  6. J Leipzig. “A review of bioinformatic pipeline frameworks”. Briefings in Bioinformatics 3 (2017): 530-536.
  7. J Dahlberg., et al. “Arteria: An automation system for a sequencing core facility”. Gigascience 12 (2019): giz135.
  8. M Kotliar., et al. “CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language”. Gigascience7 (2019): giz084.
  9. J Bedő. “Bio Shake: a Haskell EDSL for bioinformatics workflows”. Peer Journal 7 (2019): e7223.
  10. G Wang and B Peng. “Script of Scripts: a pragmatic workflow system for daily computational research”. PLoS Computational Biology 2 (2019): e1006843.
  11. M Joppich and R Zimmer. “From command-line bioinformatics to bioGUI”. Peer Journal 7 (2019): e8111.
  12. U Saeed and Z Usma. “Biological sequence analysis”. In Computational Biology, Codon Publications (2019).
  13. TW Tan., et al. “A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the ‘-omics’ era”. BMC Genomics3 (2009): S36.
  14. MA Wilson Sayres., et al. “Bioinformatics core competencies for undergraduate life sciences education”. PLoS ONE6 (2018): e0196878.
  15. RE Tractenberg., et al. “The mastery rubric for bioinformatics: a tool to support design and evaluation of career-spanning education and training”. PLoS ONE11 (2019): e0225256.
  16. JX Lim., et al. “Sequence composition”. In Encyclopedia of Bioinformatics and Computational Biology, Elsevier (2019): 323-326.
  17. JH Kim and MH Ling. “Proteome diversities among 19 archaebacterial species”. Acta Scientific Microbiology 5 (2019): 20-27.
  18. A Maitra and MH Ling. “Codon usage bias and peptide properties of Pseudomonas balearica DSM 6083T”. MOJ Proteomics and Bioinformatics2 (2019): 27-39.
  19. M H Ling. “Island: a simple forward simulation tool for population genetics”. Acta Scientific Computer Sciences2 (2019): 20-22.
  20. MH Ling. “RANDOMSEQ: Python command‒line random sequence generator”. MOJ Proteomics and Bioinformatics 4 (2018): 206-208.
  21. MH Ling. “SEcured REcorder BOx (SEREBO) based on blockchain technology for immutable data management and notarization”. MOJ Proteomics and Bioinformatics6 (2018): 169-174.
  22. MH Ling. “Draft implementation of a method to secure data by file fragmentation”. Acta Scientific Computer Sciences2 (2019): 10-13.
  23. PJA Cock., et al. “Biopython: freely available Python tools for computational molecular biology and bioinformatics”. Bioinformatics11 (2009): 1422-1423.
  24. O Carugo. “Frequency of dipeptides and antidipeptides”. Computational and Structural Biotechnology Journal 11 (2013): e201308001.
  25. JR Lobry and C Gautier. “Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes”. Nucleic Acids Research15 (1994): 3174-3180.
  26. K Guruprasad., et al. “Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence”. Protein Engineering, Design and Selection2 (1990): 155-161.
  27. J Kyte and RF Doolittle. “A simple method for displaying the hydropathic character of a protein”. Journal of Molecular Biology 1 (1982): 105-132.
  28. V Mauno., et al. “Accuracy of protein flexibility predictions”. Proteins: Structure, Function, and Bioinformatics2 (1994): 141-149.
  29. TF Smith and MS Waterman. “Identification of common molecular subsequences”. Journal of Molecular Biology 1 (1981): 195-197.
  30. SB Needleman and CD Wunsch. “A general method applicable to the search for similarities in the amino acid sequence of two proteins”. Journal of Molecular Biology 3 (1970): 443-453.
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Citation

Citation: Maurice HT Ling. “SeqProperties: A Python Command-Line Tool for Basic Sequence Analysis". Acta Scientific Microbiology 3.6 (2020): 103-104.



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