More information XML output
| Name | PRRN |
|---|---|
| Aliases | None |
| Description | PRRN is a multiple sequence alignment program by doubly nested randomized iterative method. PRRN accepts either nucleotide or protein sequences. PRRN repeatedly uses pairwise group-to-group alignment to improve the overall weighted sum-of-pairs score at each iterative step, where the pair weights are introduced to correct for uneven representations of the sequences to be aligned. The strategies of PRRN work most effectively for refining a crude alignment obtained by other more rapid methods, e.g. progressive alignment. (Summarized from the original site) |
| Type | Tool |
| Main Institutes of management | Graduate School of Informatics, Kyoto University |
| Country of the Institute | Japan |
| URL of the site | http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/prrn/index.html |
| Interface | CUI (Character User Interface), Web |
| Input example | Under investigation |
| Keyword |
multiple alingment
|
| Amount of the all data for download（Mbyte） | Method to obtain the all data. | 1.3 | Available at the top page. |
| External resources (databases) in building the product. | None |
| Data type | DNA, amino acid sequences |
| Biological species in the main concern |
All species
|
| Conditions of use | Under investigation |
| Frequency of updates (in last two years) | 1 |
| Last date of updates (date of confirmation) | 2007/00/00 (2009/01/20) |
| Main IDs used in the products | Under investigation |
| How to make a link to get access to each IDs. | Under investigation |
| external databases to which this database/tool have links | Under investigation |
| Published papers (PubMed IDs) | [1] Berger, M.P., and Munson, P.J. (1991) "A novel randomized iterative strategy for aligning multiple protein sequences." CABIOS 7, 479-484.
[2] Gotoh, O. (1993) "Optimal alignment between groups of sequences and its application to multiple sequence alignment." CABIOS 9, 361-370.
[3] Gotoh, O. (1993) "Extraction of conserved or variable regions from a multiple sequence alignment." Proceedings of Genome Informatics Workshop IV, pp. 109-113.
[4] Gotoh, O. (1994) "Further improvement in group-to-group sequence alignment with generalized profile operations." CABIOS 10, 379-387.
[5] Gotoh, O. (1995) "A weighting system and algorithm for aligning many phylogenetically related sequences." CABIOS, 11, 543-551.
[6] Gotoh, O. (1996) "Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments." J. Mol. Biol. 264, 823-838.
[7] Gotoh, O. (1999) "Multiple sequence alignment: algorithms and applications." Adv. Biophys. 36, 159-206.
[8] Yamada, S., Gotoh, O., Yamana, H. (2006) “Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost.” BMC Bioinformatics, 7, 524.
[9] Yamada, S., Gotoh, O., Yamana, H. (2008) “Improvement in speed and accuracy of multiple sequence alignment program PRIME.” IPSJ Trans. Bioinformat., 1, 2-12. |