All About Annotation Step Of Prokayotes

Question

[wHo]

Hi, everyone! I want ask an old question. Can you help me? I have a Prokayotes genome which have been assembled by an reference sequence. Of course, there are many gaps existing. I want to do annotation such as kegg、go and so on. I am not very clear about the step of annotation. I have used glimmer3 to find orf of the sequence. What shouid I do next and next? Ok, I confused. In addtion, my teacher ask me to figure out the difference between two sequences and list the different position(orf) about function. With my existing knowledge, I can not give him the answer. Thank you a lot~

Answer 1

[Rohit]

RAST is an online tool which helps in the annotation of prokaryotic genomes... Give it a try for the start...

There are other automated annotation servers like Ensembl, NCBI Prokaryotic Genome Annotation Pipeline (PGAAP), JGI Genome Annotation Pipeline, Microbial Genome Annotation Pipeline, IGS Annotation Engine to name a few

[wHo]

What about glimmer3? Is there some software which is used in local?

[Rohit]

Glimmer, Genscan, GeneMark are some I know... It is a big list when it comes to Bioinformatics tools for prediction, its all about integrating results and marking out novel ones... Data and results are always there, it is the Analysis that counts...

[wHo]

I have read some paper. I learn it by myself. So, there are many questions existing. I just want to have a systematic learning which much like a process. Thank you for help.