Dear Members,
I am working on prokaryotic data for gene prediction. I have list of few accurate tools:
1) GENEPrimp - having issues running it. post processing tool
2) Ab initio: genemark.hmm, genemarkS, prodigal and glimmer3. I am unable to knockout either of Genemark. GenemarkS is enhanced version of genemark.hmm. One uses gibbs sampling and other viterbi algorithm. Both can give output in gff format.
How should I narrow down?
I have to work on FgeneB and EasyGenes
3) Homology Based:
a) genewise: have issues with it ,c files. I am getting ld exit error.
b) BLAST v/s BLAT:
BLAT paper says it is good for vertebrates, but after that I haven't found much on its input data type. BLAT is fast and less accurate than BLAST. It is good for homologous species.
How should I narrow down here?
Please help in this.
0 answers
No answers yet.
Log in to answer this question.
I would rephrase the question, the title is too loaded - there are not that many people that have used all three but there could be people that used one or the other. I would focus on asking feedback on which tool worked well rather than asking people to put one tool on the podium.