Related Experiment Video
Updated: Nov 2, 2025
Reliable Method for Assessing Seed Germination, Dormancy, and Mortality under Field Conditions
Published on: November 6, 2016
ALeS: adaptive-length spaced-seed design
1Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada.
Motivation:
Sequence similarity is the most frequently used procedure in biological research, as proved by the widely used BLAST program. The consecutive seed used by BLAST can be dramatically improved by considering multiple spaced seeds. Finding the best seeds is a hard problem and much effort went into developing heuristic algorithms and software for designing highly sensitive spaced seeds.
Results:
We introduce a new algorithm and software, ALeS, that produces more sensitive seeds than the current state-of-the-art programs, as shown by extensive testing. We also accurately estimate the sensitivity of a seed, enabling its computation for arbitrary seeds.
Availabilityand Implementation:
The source code is freely available at github.com/lucian-ilie/ALeS.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Related Concept Videos
02:27Trihybrid Crosses
Some of Mendel’s crosses examined three pairs of contrasting characteristics. Such a cross is called a trihybrid cross. A trihybrid cross is a combination of three individual monohybrid crosses. For example, plant height (tall vs. short), seed shape (round vs. wrinkled), and seed color (yellow vs. green).
The F1 generation plants of a trihybrid cross are heterozygous for all three traits and produce eight gametes. Upon self-fertilization, these gametes have an equal...
01:18Dihybrid Crosses
02:33Seed Structure and Early Development of the Sporophyte
01:20Monohybrid Crosses