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PIP: a database of potential intron polymorphism markers
- Source :
- Bioinformatics. 23:2174-2177
- Publication Year :
- 2007
- Publisher :
- Oxford University Press (OUP), 2007.
-
Abstract
- Motivation: With the recent progress made in large-scale plant functional genome sequencing projects, a great amount of EST (express sequence tag) data is becoming available. With the help of complete genomic sequence information of model plants (rice and Arabidopsis), it is possible to predict the joints between adjacent exons after splicing (or termed ‘intron positions’ for short) in homologous ESTs of other plants. This would allow developing potential intron polymorphism (PIP) markers in these plants by designing primers in exons flanking the target intron. Results: We have extracted a total of 57 658 PIP markers in 59 plant species and created a web-based database platform named PIP to provide detailed information of these PIP markers and homologous relationships among PIP markers from different species. The platform also provides a function of online designing of PIP markers based on cDNA/EST sequences submitted by users. With evaluations performed in silico, we have found that the intron position prediction is highly reliable and the polymorphism level of PIP markers is high enough for practical need. Availability: http://ibi.zju.edu.cn/pgl/pip/ Contact: wuwr@zju.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
- Subjects :
- Genetic Markers
musculoskeletal diseases
Statistics and Probability
DNA, Plant
In silico
Molecular Sequence Data
Information Storage and Retrieval
Biology
computer.software_genre
Polymorphism, Single Nucleotide
Biochemistry
DNA sequencing
Evolution, Molecular
Exon
Complementary DNA
Arabidopsis
Databases, Genetic
Molecular Biology
Genetics
Base Sequence
Database
fungi
Intron
Chromosome Mapping
Genetic Variation
food and beverages
biology.organism_classification
Introns
Computer Science Applications
Computational Mathematics
Computational Theory and Mathematics
RNA splicing
lipids (amino acids, peptides, and proteins)
computer
Genome, Plant
Function (biology)
Subjects
Details
- ISSN :
- 13674811 and 13674803
- Volume :
- 23
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....3e874059d812d3053695173bb5ffe6ba