More information XML output
| Name | ALN |
|---|---|
| Aliases | None |
| Description | Aln is a program for aligning a pair of nucleotide or amino acid sequences or alignments. Aln can even align a nucleotide sequence and a single or a group of protein sequences. This can be used to predict eukaryotic gene structures (protein-coding exons) based on sequence homology with known protein sequences. |
| 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/aln/ |
| Interface | CUI (Character User Interface), Web |
| Input example | After clicking "Online Server", select one of the "Sequence Type". For each sequence 1 and 2, upload or paste your sequence(s), and input sequence type (G, D, or P). Optionally, you check "Complement" when you analyze the complementary strand of your sequence(s), and enter start and end position in your sequence to be aligned. In the step 2, change the parameters if you need. Finally you enter the "Submit" button. |
| Keyword |
align | gene prediction
|
| Amount of the all data for download（Mbyte） | Method to obtain the all data. | 1.2 | Available at the top page |
| External resources (databases) in building the product. | Under investigation |
| 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 | なし |
| How to make a link to get access to each IDs. | None |
| external databases to which this database/tool have links | Under investigation |
| Published papers (PubMed IDs) | [1] Gotoh, O. (1982) "An improved algorithm for matching biological sequences." J. Mol. Biol. 162, 705-708.
[2] Gotoh, O. (1990) "Optimal sequence alignment allowing for long gaps." Bull. Math. Biol. 52, 359-373.
[3] Gotoh, O. (1993) "Optimal alignment between groups of sequences and its application to multiple sequence alignment." CABIOS 9, 361-370.
[4] Gotoh, O. (1994) "Further improvement in group-to-group sequence alignment with generalized profile operations." CABIOS 10, 379-387.
[5] Gotoh, O. (1998) "Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes." Mol. Biol. Evol. 15, 1447-1459.
[6] Gotoh, O. (2000) "Homology-based gene structure prediction: simplified matching algorithm by the use of translated codon (tron) and improved accuracy by allowing for long gaps." Bioinformatics, 16, 190-202. |