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Aptaligner: Automated Software for Aligning Pseudorandom DNA X-Aptamers from Next-Generation Sequencing Data
- Source :
- Biochemistry
- Publication Year :
- 2014
- Publisher :
- American Chemical Society, 2014.
-
Abstract
- Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient. This is particularly true for X-aptamers containing specialty bases (W, X, Y, Z, ...) that are identified by special encoding. Thus, we sought an automated program that uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov modeling techniques to provide improved alignments. Aptaligner provides this feature as well as length error and noise level cutoff features, is parallelized to run on multiple central processing units (cores), and sorts sequences from a single chip into projects and subprojects.
- Subjects :
- Pseudorandom number generator
Genetics
Rapid Report
Sequence analysis
business.industry
Aptamer
SELEX Aptamer Technique
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Biology
Aptamers, Nucleotide
Markov model
Biochemistry
DNA sequencing
Random Allocation
Software
Feature (computer vision)
Encoding (memory)
business
Algorithm
Subjects
Details
- Language :
- English
- ISSN :
- 15204995 and 00062960
- Volume :
- 53
- Issue :
- 22
- Database :
- OpenAIRE
- Journal :
- Biochemistry
- Accession number :
- edsair.doi.dedup.....ec4f801372c3f430472109592e456e39