| I. Transcriptome assembly |
| 1 |
Newbler |
De novo assembly |
- |
| II. Annotation tool |
| 1 |
NCBI BLAST |
Preliminary annotation of transcripts |
www.ncbi.nlm.nih.gov/ |
| III. Gene prediction |
| 1 |
FGENESH |
Prediction of open reading frame |
http://www.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind |
| 2 |
AUGUSTUS |
Prediction of open reading frame |
http://bioinf.uni-greifswald.de/augustus/submission.php |
| IV. Sequence analysis |
| 1 |
CDD |
Identification of conserved domain |
http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi |
| 2 |
Pfam |
Protein family classification |
http://pfam.xfam.org/search |
| V. Fold analysis |
| 1 |
PSIPRED |
Fold recognition |
http://bioinf.cs.ucl.ac.uk/psipred/ |
| 2 |
PHYRE2 |
Fold recognition |
http://www.sbg.bio.ic.ac.uk/phyre2/ |
| 3 |
GenTHREADER |
Fold recognition |
http://bioinf.cs.ucl.ac.uk/psipred/ |
| VI. Gene Ontology |
| 1 |
Gene Ontology |
Annotation |
http://geneontology.org/ |
| VII. Phylogenetic analysis |
| 1 |
MEGA5 |
|
http://www.megasoftware.net/ |
| VIII. Protein-protein interaction |
| 1 |
STRING |
To find out interacting partners |
http://string-db.org/ |
| IX. Expression analysis |
| 1 |
qRT-PCR |
To analyze the functional significance |
- |
