Data from: High evolutionary turnover of satellite families in Caenorhabditis


Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title satfind
Downloaded 16 times
Description Satfind has been designed to find satellites that contain patterns (the seed) of length L (<15) that appear at least n times in a DNA subsequence of length N. Once a satellite is found the search is continued until no more seeds are found in N bases, then the search may continue beyond the original length N. Each seed defines a possible repeat that ends at the start of the next seed. The satellite is accepted if we are able to select a percentage p of possible repeats (selected repeats) with the same length and, in this case, these selected repeats become the repeats of the satellite. The first one is chosen as the representative repeat of the satellite.
Download satfind.tar (307.2 Kb)
Download README (2.139 Kb)
Details View File Details
Title malig: DNA multialignment software
Downloaded 7 times
Description Malig has been implemented in C. Just untar malig.tar and run the make file utility. Malig has been designed to global align DNA sequences with similar length using the progressive multialignment method whose pairwise alignment uses the dynamic programming algorithm designed by Needlema and Wunsch, both with the affine gap penalty function. As a progressive multialignment method malig first computes the similarity score between all pairs of sequences. This computation is made under the following criteria: Normalized score: the idea is that a multialignment of identical sequences has to be scored one. Reverse sequences: the input file is increased by adding the reverse sequences. Cycle permutations: to compute the score between two sequences, we choose the cycle permutation of the second one with the greatest score, and this cycle is applied when the multialignment is built. Then the progressive multialignment is started. Recall that in a classic multialignment algorithm this process finishes when all sequences are aligned. In our case the process finish when the score is smaller than a similarity threshold (input parameter).
Download malig.tar (204.8 Kb)
Download README (2.139 Kb)
Details View File Details

When using this data, please cite the original publication:

Subirana JA, Alba MM, Messeguer X (2015) High evolutionary turnover of satellite families in Caenorhabditis. BMC Evolutionary Biology 15: 218.

Additionally, please cite the Dryad data package:

Subirana JA, Alba MM, Messeguer X (2015) Data from: High evolutionary turnover of satellite families in Caenorhabditis. Dryad Digital Repository.
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: