SATFIND specifications
Information
| Unique identifier | OMICS_11576 |
|---|---|
| Name | SATFIND |
| Interface | Web user interface |
| Restrictions to use | None |
| Input data | DNA sequence(s) |
| Input format | FASTA |
| Output data | The output of the program includes: (i) the sequence of 10 bases which has been found repeated at least 10 times in a region of 2 Kb; (ii) the number of tandem repeats found; (iii) the genome coordinates of the region which contains the satellite; (iv) the length of genome covered by the satellite, which may be longer than the initial 2 Kb, since the program continues searching when repeats are found beyond the end of the 2 Kb. The length detected by the program occasionally is longer than the actual satellite. It happens when the repeated 10 base motif is found embedded in unrelated sequences in the neighborhood of the satellite; (v) the most frequent size of the motif repeated in tandem in the satellite; (vi) in a second output file we give the sequence of the repeated motifs in all satellites. If the repeated motifs show a large variation in size, the satellite is eliminated. In this work we have chosen to accept only those satellites in which 40% of the motifs have a similar size. Thus we eliminate from the output some satellites which are very irregular. |
| Computer skills | Basic |
| Stability | Stable |
| Maintained | Yes |
Maintainer
- person_outline Juan A. Subira <>
Publication for SATFIND
2013 PLoS One
PMCID: 3634726
PMID: 23638010
DOI: 10.1371/journal.pone.0062221
SATFIND institution(s)
Departament d’Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain; Departament de Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya, Barcelona, Spain
SATFIND funding source(s)
This work was supported in part by grants BFU2009-10380 and TIN2010-21062-C02-01 from the Ministerio de Innovación y Ciencia, Spain.
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