ArticleBMC bioinformatics2002
Making sense of EST sequences by CLOBBing them.
Article in BMC bioinformatics, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed.
- KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella.BMC genomics · 2013Article
- A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags.BMC research notes · 2012Article
- A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation.PLoS neglected tropical diseases · 2012Article
- Spliceosomal intron size expansion in domesticated grapevine (Vitis vinifera).BMC research notes · 2011Article
- Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak.BMC genomics · 2010Article
- Exploiting a wheat EST database to assess genetic diversity.Genetics and molecular biology · 2010Article
- PEACE: Parallel Environment for Assembly and Clustering of Gene Expression.Nucleic acids research · 2010Article
- Survey of transcripts expressed by the invasive juvenile stage of the liver fluke Fasciola hepatica.BMC genomics · 2010Article
- Quantitative gene expression profiles in real time from expressed sequence tag databases.Gene expression · 2010Article
- Next generation transcriptomes for next generation genomes using est2assembly.BMC bioinformatics · 2009Article
- Analysis of expressed sequence tags and identification of genes encoding cell-wall-degrading enzymes from the fungivorous nematode Aphelenchus avenae.BMC genomics · 2009Article
- A family of diverse Kunitz inhibitors from Echinococcus granulosus potentially involved in host-parasite cross-talk.PloS one · 2009Article
- k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage.Bioinformatics (Oxford, England) · 2009Article
- EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data.BMC bioinformatics · 2009Article
- Characterisation of novel protein families secreted by muscle stage larvae of Trichinella spiralis.International journal for parasitology · 2009Article
- MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences.BMC genomics · 2009Article
- On the extent and origins of genic novelty in the phylum Nematoda.PLoS neglected tropical diseases · 2008Article
- Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus.BMC genomics · 2008Article
- Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: a genomic resource for studying agricultural pests.BMC genomics · 2008Article
- Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature.BMC genomics · 2008Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundExpressed sequence tags (ESTs) are single pass reads from randomly selected cDNA clones. They provide a highly cost-effective method to access and identify expressed genes. However, they are often prone to sequencing errors and typically define incomplete transcripts. To increase the amount of information obtainable from ESTs and reduce sequencing errors, it is necessary to cluster ESTs into groups sharing significant sequence similarity.
resultsAs part of our ongoing EST programs investigating 'orphan' genomes, we have developed a clustering algorithm, CLOBB (Cluster on the basis of BLAST similarity) to identify and cluster ESTs. CLOBB may be used incrementally, preserving original cluster designations. It tracks cluster-specific events such as merging, identifies 'superclusters' of related clusters and avoids the expansion of chimeric clusters. Based on the Perl scripting language, CLOBB is highly portable relying only on a local installation of NCBI's freely available BLAST executable and can be usefully applied to > 95 % of the current EST datasets. Analysis of the Danio rerio EST dataset demonstrates that CLOBB compares favourably with two less portable systems, UniGene and TIGR Gene Indices.
conclusionsCLOBB provides a highly portable EST clustering solution and is freely downloaded from: http://www.nematodes.org/CLOBB
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