I am interested in detecting structures in a de novo transcriptome I am in the process of annotating. I am interested in seeing if there are any tools that I could use to rapidly identify structural motifs in my transcripts, especially those that do not have orthologs in other species. I am expecting a large amount of data so I was wondering if anyone has any experience doing this sort of annotation in a programmatic way. What would be a reasonable place to begin?
1 answer
You may want to use Annocript. It was just published on Bioinformatics and permits annotation of any type of transcriptome (both nucleotides and peptides). It is a pipeline that runs BLAST programs and gives the best HIT against SwissProt and TrEMBL or UniRef, CDD domains, rFam. Annotation also provide GO terms association with proteins and/or domains, Enzyme and Pathwyas. Moreover it also presents which transcripts could be putative lncRNAs. It gives a lot of outputs: a complete table with the annotation, plots and statistics, blast output in GFF3 format, fasta file with the putative coding and long non coding sequences.
The program is straightforward to use and open source. Here is the paper, and here is the software.
•
written
by
francescomusacchia
Log in to answer this question.
-
Make a reference transcriptome for nonmodel organism
written by abantika2005 •
-
how to define more stringent parameters for the snoscan to indentify snoRNA target on rRNA?
written by PK •
-
finding rna motifs in the 3' or 5' regions using RNASeq using DESeq2 genesets
written by lavanya.kannan •
-
finding rna motifs in the 3' or 5' regions using RNASeq using DESeq2 genesets
written by lavanya.kannan •
-
Well characterized circular RNA structure
written by ccag •
-
Mixed Platforms for de novo Transcriptome and Differential Expression
written by pld
-
Best Reciprocal BLAST and Alternative Transcripts
written by pld
-
Mining Ortholog Cliques
written by pld
-
How Do I Compare Sequence Quality/Coverage Between Two Species?
written by pld
-
Transitioning Database From Expression Microarrays To Rna-Seq
written by pld
