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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

SATFIND in publications

 (3)
PMCID: 5765664
PMID: 29325570
DOI: 10.1186/s12915-017-0473-4

[…] 4fig. 5, the final assembly contained a much greater diversity of repeat sequences than seen in the wtsi reference sequence (fig. ). the repeat with the longest unit length (535 bp) as determined by satfind [], corresponded to a region with ten tandem copies (fig. ) of an 5s rrna gene interspersed with an snrna gene, the source of the spliced leader rna that is added to many transcripts. […]

PMCID: 5748669
PMID: 29182550
DOI: 10.3390/genes8120351

[…] briggsae; to understand the evolutionary dynamics of their tandem repeat sequences (satellites), as a result of evolution from the unisexual ancestor. we take advantage of the previously developed satfind program to build satellite families defined by a consensus sequence. the relative number of satellites (satellites/mb) in c. nigoni is 24.6% larger than in c. briggsae. some satellites in c. […]

PMCID: 4595182
PMID: 26438045
DOI: 10.1186/s12862-015-0495-x

[…] from several species in the group offer a unique opportunity to better understand the evolutionary dynamics and the functional role of these sequences. we take advantage of the previously developed satfind program to study the satellites in four caenorhabditis species and investigate these questions., the identification and comparison of satellites is carried out in three steps. first we find […]


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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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