A blog about free research software, alternative to commercial paid software.

One way to help people is to share your knowledge with those who could benefit from it. As a researcher , constant effort to solve scientific problems have exposed me to various scientific resources that can be accessed free of charge. Especially these knowledge is useful to labs and institution unable to access expensive software or novice users due to lack of expertise. In this blog, I have provided a comprehensive list of freely available softwares, alternative to commercial software. I shall share with you all that I have learned, as I make the changes or learn something new, I shall document them. Hope this blog will help those finding the way………….

Research software and books

Apr 16, 2011

Interactive software tool for optimal sequence alignments with dynamic programming.


Dynamic programming (DP) is an optimizing strategy commonly used in various discipline in science. It is widely used in biology to calculate optimal alignment between pairs of protein or DNA sequences. DP is so important, that it is core of many software applications available today for sequence analysis. DP algorithm is essential topic in many undergraduate and graduate bioinformatics course. Although simple in formulation, DP is not that easy for students to learn.

Sequence alignment teacher (SAT) is a simple software, which interactively calculates the DP matrix in real time. Also SAT visually illustrates the consequence of tweaking the various parameters of the algorithm.


1) The user can visualize and modify the values in the similarity matrix and the gap opening/extension penalties.

2) The user can generate a report of the current data and results in PDF format.

3) The user can get filled DP matrix with the backtrace path of the currently selected optimal alignment.


Ibarra, I., & Melo, F. (2010). Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming Bioinformatics, 26 (13), 1664-1665 DOI: 10.1093/bioinformatics/btq252

Papermaker: An easy way to validate scientific publication.



A well written scientific publication has high chance of getting through the peer review process. Research publication has to comply with standards concerning the document format, the use of language and the citation of prior work. Once the manuscript is written in loosely structured natural language by the researcher, the manuscript has to be validated for

1) Proper use of acronyms and their definitions.

2) Spellings

3) GO and MeSH terms

4) References

Papermaker receives a scientific manuscript via web interface, analyses the publication, evaluates consistency parameters and interactively delivers feedback to the author. It performs the task of spelling checks, analyses the proper use of acronyms and their definitions. Further it provides Gene Ontology (GO) and Medline Subject Headings (MeSH) categorization of text passages, the retrieval of relevant publications from public scientific literature repositories, and the identification of missing or unused references. Thus automated analysis of scientific literature can support authors in writing their manuscripts.

Rebholz-Schuhmann, D., Kavaliauskas, S., & Pezik, P. (2010). PaperMaker: validation of biomedical scientific publications Bioinformatics, 26 (7), 982-984 DOI: 10.1093/bioinformatics/btq060