MPscan
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Application data |
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| Created by | E. Rivals, L. Salmela, P. Kiiskinen, P. Kalsi, J. Tarhio |
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| Biological application domain(s) | Genomics, Transcriptomics |
| Principal bioinformatics method(s) | Read mapping |
| Technology | Illumina |
| Created at | CNRS, Université Montpellier (FR); Aalto University (FI) |
| Maintained? | Maybe |
| Input format(s) | FASTA |
| Output format(s) | raw, one read per line |
| Programming language(s) | C++ |
| Operating system(s) | Linux, Mac OS X |
Summary: MPscan (multi-pattern scan) is a program for mapping short reads (<30bp) exactly on a set of reference sequences (eg, a genome) without indexing the reference. MPscan performs only exact mapping (no substitution, nor indels), is fast (optimal complexity), and easy to use.
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Description
MPscan is designed for reads of short length and having all the same length. It works for longer reads as well (but this is not sufficient since they likely contain errors). MPscan is guaranteed to return the correct answer (no heuristics).
MPscan was used for analysing Digital Gene Expression, Chip-Seq, SAGE and CAGE reads, in a pipeline see:
Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity N. Philippe*, A. Boureux*, L. Bréhèlin, J. Tarhio, T. Commes, E. Rivals Nucleic Acids Research (NAR) Vol. 37, No. 15 e104, doi:10.1093/nar/gkp492; 2009.
More details about the method in:
MPSCAN: fast localisation of multiple reads in genomes E. Rivals, L. Salmela, P. Kiiskinen, P. Kalsi, J. Tarhio Proc. 9th Workshop on Algorithms in Bioinformatics Lecture Notes in BioInformatics (LNBI), Springer-Verlag, Vol. 5724, p. 246-260, 2009.
Links
- MPscan Analysis server [ edit link ]
- MPscan Homepage [ edit link ]
- MPscan Publication full text [ edit link ]
References
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