Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

(2013) Michele Vidotto et al.   BMC GENOMICS

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

The Transcriptome Analysis and Comparison Explorer—T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms

(2012) E. E. R. Philipp et al.   BIOINFORMATICS

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

UniPathway: a resource for the exploration and annotation of metabolic pathways

(2011) Anne Morgat et al.   NUCLEIC ACIDS RESEARCH

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis

(2009) Roberto T Arrial et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

annot8r: GO, EC and KEGG annotation of EST datasets

(2008) Ralf Schmid et al.   BMC BIOINFORMATICS