Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP
نویسندگان
چکیده
منابع مشابه
Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data.
We have developed a computer based method to identify candidate single nucleotide polymorphisms (SNPs) and small insertions/deletions from expressed sequence tag data. Using a redundancy-based approach, valid SNPs are distinguished from erroneous sequence by their representation multiple times in an alignment of sequence reads. A second measure of validity was also calculated based on the coseg...
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BACKGROUND AND AIMS Banana (Musa acuminata) is a crop contributing to global food security. Many varieties lack resistance to biotic stresses, due to sterility and narrow genetic background. The objective of this study was to develop an expressed sequence tag (EST) database of transcripts expressed during compatible and incompatible banana-Mycosphaerella fijiensis (Mf) interactions. Black leaf ...
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Bioinformatics — the application of computer technology to the management of biological information — is essential to deciphering the genetic code of life. Novel approaches to genome sequencing, such as microarray technology, high-performance supercomputing and computational simulations in high-throughput DNA analysis have led to an explosion of genomic data available. Accurate genomic assembly...
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Expressed Sequence Tag (EST) sequencing is a highly efficient technique that samples expressed genes required for most cellular functions. While this is a well-studied problem and many software tools have been developed, large-scale EST clustering has previously been pursued through incremental approaches, a pipeline of programs and manual efforts to achieve a modest degree of parallelism. Here...
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Salicornia spp is one of the most salt-tolerant vascular plants and is native to salt marshes and estuaries. We developed expressed sequence tag derived-simple sequence repeat (EST-SSR) markers for estimating genetic diversity and marker-assisted Salicornia breeding. Six polymorphic EST-SSRs of 40 detected 27 alleles, ranging from three to five alleles per locus. The average number of alleles p...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2003
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btf881