Could anyone indicate the best (or most used) software to map stripped ESTs to a predicted transcriptome (or even predicted proteins) from a model organism genome?
I would like to build contigs from Roche 454 ESTs using the genome of a close model organism. I have been told mapping to genome is interesting however that because of the presence of introns, many generated contigs are artifacts, and often of huge size (over 50Kbp). A friend told me he had interesting results from mapping ESTs to predicted proteins from a model organism using CLC Workbench.
Does anyone have any suggestions?
Thanks Giuseppe, I see what you mean. I think some softwares have a special "map to genome" function which also enables the user to extract the consensus sequences form the mapping. Yet I am not sure which function to use if I am to map ESTs to predicted proteins/transcripts from a reference genome... Not sure if it is the same procedure with same softwares. What do you think? My main concern is "fishing" only the exons from the consensus, that is why we are opting for predicted sequences.
Hi all, an idea could be to use GMAP to map the 454 ESTs to the genome and then create the transcriptome with cufflinks. Best
Hi all, I am still thinking about the best solutions. Thanks to everyone for the useful tips. Let me just clarify a few aspects: I want to map 454 reads to a predicted transcriptome. This means my reads are long and I do not have a reference proteome -- although I do can generate a reference proteome in silico from predicted transcripts from reference genome.
I wish to avoid mapping ESTs directly to genome as previous experience shows it yields very long (=not real) contigs because introns are mapped. I have used CLC for this.
I would thus like to know in your opinion would be the best software to map ESTs to predicted transcriptome as to get equivalent contigs,
I am thinkng about using MIRA or maybe gsMapper with the annotated genome...
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