Suppose i have a DNA sequence and i want to find transcription strat site, CDS, poly A signal etc., which software will be useful to find this out?
you can use this free software
http://exon.gatech.edu/
You can choose any program from this website that get matched with your source of dna sequence.
you can use GenomeThreader Gene Prediction Software. it will be helpful to you.
in NCBI ..... Gene bank and unigene are also helpful to you.
Hi Tushar,
In this link (http://www.expasy.org/genomics) maybe you can find a tool useful for you. For example, SSA software package for the analysis of nucleic acid sequence motifs or another programs in this website.
Regards,
Hi Tushar,
There are many freely available softwares for this purpose. You can use any of them according to your need.
For eukaryotic gene prediction:
GrailEXP (http://compbio.ornl.gov/Grail-1.3/)
GeneMark-E (http://exon.biology.gatech.edu/)
HMMgene (http://www.cbs.dtu.dk/services/HMMgene/)
GENSCAN(http://genes.mit.edu/GENSCAN.html)
GenomeScan(http://genes.mit.edu/genomescan.html)
TwinScan - http://mblab.wustl.edu/nscan/submit/ (requires Login)
Augustus – http://bioinf.unigreifswald.de/augustus/submission/
For prokaryotic gene prediction:
Glimmer 3.02 - http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi
GeneMark.hmm- http://opal.biology.gatech.edu/GeneMark/gmhmm2_prok.cgi
Other than that you can find more softwares for gene predictions for eukaryotes and prokaryotes using:
www.geneprediction.org
I hope this will help you.
Thanks,
Saurabh
GeneMark is best known for this. I found its results most reliable, while predicting it does asks for model organism which characterizes its performance: http://exon.gatech.edu/GeneMark/metagenome/Prediction/
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