Generalized methods rely extensively on data mining of sequence information, gene expression datasets, functional annotations and/or protein protein interactions.
The mining of sequence patterns, also called motifs, is one of the most important tasks in protein sequence analysis and continues to be an active topic of research.
Thus, the trimmed dbEST sequences present some obstacles for data quality control and validation of error-prone EST sequences, as well as data mining of sequence features with potential biological meanings whose detection relies on the terminus information in ESTs.
Identifying sets of homologous transcripts in other Pinaceae has improved in the recent years through efficient mining of sequence databases e.g. [ 66, 67] and because of large sets of EST sequences for several species [ 22- 25, 40].
Blast2GO is a bioinformatic tool for the GO-based annotation and data mining of sequence sets for which no GO annotation is yet available, which has proven to be effective in the functional characterization of plant sequence data [ 43].
Using the MIRA-based assembly and SNP mining of sequence data obtained from microarray-captured genomic DNA samples, we identified 4,536 SNPs among the four eggplant lines, 'AE-P03'LS-1934 'LS-1934GR112-8'WCGR112-8 'WCGR112-8ro'.
The present study contributes to our knowledge on fungal DyPs by mining the sequenced genome of P. ostreatus for enzymes of this new peroxidase family.
The time-consuming and expensive process of developing enriched genomic libraries and the subsequent sequencing and seeking of the simple sequence repeats is now often replaced with data mining of expressed sequence tag (EST) libraries to give a rapid, efficient and low-cost alternative for identifying microsatellites in plant species.
Recent efforts to develop new markers in cultivated tomato have been focus on single-nucleotide polymorphisms (SNPs) using in silico mining of expressed sequence tag database and experimental validation, amplicon sequencing of COS genes, hybridization to oligonucleotide array, and next-generation sequencing of transcriptome or re-sequencing of genome.
We attempted to circumvent this problem by bioinformatic mining of microsatellite sequences from a de novo-sequenced transcriptome of a butterfly (Euphydryas editha).
