Abstract：
:Expressed sequence tags (ESTs) from fungal-infected plant tissues are composed of a mixture of plant and fungal sequences. Using freely available software and tools, a novel procedure is described for distinguishing plant and fungal DNA sequences. Although the GenBank non-redundant (NR) database is larger and therefore one would presume that BLASTX analysis of it would be more accurate, superior resolution of 700 randomly selected fungal ESTs was found with Standalone TBLASTX analyses with a local matching database composed of a plant and a fungal genome. Standalone TBLASTX analyses of 3,983 ESTs from nine different fungal-infected plant EST libraries also proved to be superior in identifying the origin of sequences as either plant or fungal compared to GenBank BLASTX analysis. Standalone TBLASTX with a matching database comprised of a single plant and a single fungal genome appears to be a faster and more accurate method than BLASTX searches of the GenBank non-redundant database to distinguish fungal and plant sequences in mixed EST collections.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Hsiang T,Goodwin PHdoi
10.1016/s0167-7012(03)00067-8subject
Has Abstractpub_date
2003-09-01 00:00:00pages
339-51issue
3eissn
0167-7012issn
1872-8359pii
S0167701203000678journal_volume
54pub_type
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