Tool:How to find the Genes present in the sequence?

Question

[div]

Hi All,

I have sequence (multi-fasta) from two assemblers MIRA and SPAdes and the result of these two assembler were merged by using CISA tool and now I have to find the list of genes present in the merged Sequence. Please help me out and suggest tool or program gives the best result for this job.

Thanks in advance

[venu]

Can you provide a sample of your final file, just to check how it looks like and what tool to use.

[div]

@ Venu...Here is the sample of final file...:)

Answer 1

[Antonio R. Franco]

You don't mention what organism are you working with, but you have several choices

• You can use one of the many annotation services that are available, such as the NCBI WGS annotation Service that accepts both complete and incomplete genomes.
• A Google search make the magic of finding more automatic and free annotation services, such as the RAST service for prokaryotic
• If your assembly contains too many short contigs, Blast2Go can be interesting to use
• But I insist. These are only two of them, but some more are available

[div]

@ Antonio... I am working on Staphylococcus aureus strains which cause Diabetic Foot Ulcer....:)

Answer 2

[HG]

Have a look

http://en.wikipedia.org/wiki/List_of_gene_prediction_software

Answer 3

[Bioinformatics_NewComer]

If I may add, GeneMarkS/GeneMark (well suited for prokaryotes) could be another choice. If you plan to go for annotation too, you might want to look at Prokka. Prokka installation is crazy.