Perl/Bio-Perll: A Bioinformatics toolkit

Perl Bioperl Image

Perl is an interpreted programming language and this language easily gasped by newcomers of bioinformatics field. It connects the software applications together into sequence analysis pipelines, converts the file format and extracts the information from output of analyzed programs. Bioperl is a collection of Perl modules and provides easy to use, stable and consistent interface for bioinformatics application programmers. It is an open source software projects supported by Open Bioinformatics Foundation. It started in 1995 by a group of scientists tired of rewriting BLAST and sequence parsers for various formats. Bioperl has been used worldwide in small academic labs and large pharmaceutical companies since 1998. It is the oldest, most downloaded package among bioinformatics packages currently in use.

What makes Bioperl so useful for Bioinformatics???

Bioperl includes a wide array of utilities for biological and bioinformatics analysis. Utilities including databases used for bioinformatics information, analysis routines for genomics, proteomics, and evolutionary studies. It is capable of analysing the results from bioinformatics programs such as BLAST, Tcoffee, GenScan and ClustalW. We can do assessing the sequence from local and remote databases, transforming formats of database/file records, manipulating the individual sequences, searching for similar sequences, creating and manipulating sequence alignments, searching for gene and other structure on genomic DNA and developing machine readable sequence annotation with the help of Bioperl. The Bioperl modules have been used to reduce otherwise complex tasks to only few lines of code.  The best solution for bioinformatics problem is hybrid of multiple tools. These tools written in different programming languages like C, Java and Python, can be used in a Perl program simply by invoking them. Bioperl provides software layer that can populate a database with the sequence information that can be assessed and used to generate an interactive graphical interface provided by Biojava toolkit.

Bioperl will perform better than Biojava when processing small data set. It is very powerful for string manipulation, compared to Biopython and Biojava. It requires shortest lines of source code as compared to Biopython and Biojava. In future Bioperl will continue to evolve, addressing the more aspects of bioinformatics.

References

  1. Stajich, Jason E., David Block, Kris Boulez, Steven E. Brenner, Stephen A. Chervitz, Chris Dagdigian, Georg Fuellen et al. “The Bioperl toolkit: Perl modules for the life sciences.” Genome research12, no. 10 (2002).
  2. Ryu, Tae-Wan. “Benchmarking of BioPerl, Perl, BioJava, Java, BioPython, and Python for primitive bioinformatics tasks and choosing a suitable language.” International Journal of Contents5, no. 2 (2009).
  3. Crossman, Colin, and Arti K. Rai. “A Brief History of BioPerl.” (2005).
Share This Article :

Related Posts

Comments (27)

  1. turkce says:

    There is evidently a lot to know about this. I think you made various nice points in features also. Gwynne Justinian Ulani

  2. turkce says:

    Hey there, You have done a great job. I will certainly digg it and personally recommend to my friends. I am sure they will be benefited from this website. Yolande Meyer Akers

  3. turkce says:

    Following the thesis, you should provide nistsi.response.amsterdam/coursework/evils-of-war-essay.html a mini-outline which previews the examples you will use to support uaral.essay.amsterdam/article-review/uses-of-money-essay.html your thesis in the rest of the essay. Not only does this tell the reader what to expect in the paragraphs to come but ghagin.essay.amsterdam/thesis/german-essay-writing.html it also gives them a clearer understanding of what the essay is about. Jonell Nester Etrem

  4. turkce says:

    Greetings! Very helpful advice in this particular post! It is the little changes which will make the greatest changes. Thanks a lot for sharing!| Krystalle Alvin Bevan

  5. turkce says:

    My brother recommended I might like this blog. He was totally right. This post truly made my day. You can not imagine simply how much time I had spent for this information! Thanks! Raeann Cheston Leblanc

  6. turkce says:

    Hello! Do you know if they make any plugins to protect against hackers? Fanchette Nigel Gerhardine

  7. turkce says:

    Asking questions are genuinely nice thing if you are not understanding something totally, but this piece of writing gives nice understanding even.| Eartha Thorstein Halle

  8. turkce says:

    Great article! We are linking to this great article on our site. Marjy Luciano Matthei

  9. turkce says:

    Nice post. I learn something totally new and challenging on websites I stumbleupon on a daily basis. It will always be useful to read through articles from other authors and use something from their web sites. Rozina Gardy Bledsoe

  10. turkce says:

    Great site! I am loving it!! Will be back later to read some more. I am taking your feeds also Ethelyn Bevon Ferguson

  11. turkce says:

    You made some really good points there. I checked on the internet for more information about the issue and found most individuals will go along with your views on this web site. Deidre Andie Xaviera

  12. turkce says:

    Im grateful for the blog article. Much thanks again. Keep writing. Benny Leicester Alf

  13. turkce says:

    You should be a part of a contest for one of the highest quality websites on the web. I am going to recommend this web site! Gillan Nahum Cordula

  14. turkce says:

    we came across a cool website that you could enjoy. Take a look if you want Leshia Greggory Soulier

  15. turkce says:

    Very good post. I am going through many of these issues as well.. Cyndi Gregoor Jump

  16. turkce says:

    Hi my loved one! I wish to say that this article is amazing, nice written and include almost all significant infos. I would like to see extra posts like this . Kora Damiano Fairweather

  17. turkce says:

    I am planning on painting a vintage wooden secretary to go in my guest room. I would like to coordinate with my woodwork. The woodwork is painted with Sherwin Williams Snowbound. My walls are a silvery gray color. Which white would work best? Kameko Hilliard Johns

  18. turkce says:

    I enjoy, lead to I discovered just what I was looking for. Loreen Donn Hickie

  19. turkce says:

    A fascinating discussion is worth comment. I believe that you ought to create extra on this subject, it might not be a forbidden subject however typically people are not enough to speak on such subjects. To the next. Thanks Doralynn Caleb Crandall

  20. turkce says:

    I am not sure where you are getting your information, but great topic. Stesha Alick Park

  21. turkce says:

    I love it whenever people come together and share thoughts. Great blog, stick with it! Emilie Cecil Lucier

  22. erotik says:

    I and my buddies have been studying the excellent key points located on your web site and unexpectedly developed a horrible feeling I never thanked the website owner for them. These boys happened to be as a result excited to study all of them and have now unquestionably been loving those things. Many thanks for getting really considerate as well as for making a decision on such magnificent information most people are really wanting to understand about. My personal sincere apologies for not expressing appreciation to you earlier. Amelita Pennie Lanza

  23. Dead indited articles, Really enjoyed reading through. Kathrine Angel Lorin

  24. erotik says:

    Great blog here! Also your web site loads up fast! What web host are you using? Can I get your affiliate link to your host? I wish my site loaded up as quickly as yours lol| Martina Rutledge Herrle

  25. erotik says:

    Dead composed subject material, Really enjoyed looking at. Therine Jonas Blanch Shirl Randal Banky

  26. erotik says:

    Vim ne dicat inimicus, qui ei consul reprimique, vis homero referrentur no. Ea causae accumsan iracundia qui, tation forensibus an usu. Cu est platonem salutatus, eos argumentum definitiones et. Ei mei mollis iisque. Has ad offendit suavitate. Verla Rutger Elmira

  27. erotik says:

    Having read this I believed it was extremely informative. I appreciate you spending some time and effort to put this informative article together. I once again find myself personally spending way too much time both reading and commenting. But so what, it was still worthwhile! Bernardina Bertrand Borer

Leave A Reply

WhatsApp chat

Get Free Consultation !