SATFIND specifications
- Unique identifier:
- OMICS_11576
- Restrictions to use:
- None
- Input format:
- FASTA
- Computer skills:
- Basic
- Maintained:
- Yes
- Interface:
- Web user interface
- Input data:
- DNA sequence(s)
- 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 t
- Stability:
- Stable
SATFIND support
Maintainer
- Juan A. Subira <>
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Publications
-
(Subirana and Messeguer, 2013)
A satellite explosion in the genome of holocentric nematodes.
PLoS One.
PMID: 23638010 DOI: 10.1371/journal.pone.0062221
Institution(s)
Departament d’Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain; Departament de Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya, Barcelona, Spain
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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