Hang on..
I thought MAKER was just for ab initio. You can use that to bring together ESTs and RNA-Seq data too?
That's what I have. I'm just mapping my transcripts to the ESTs at the moment
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I am joining this project somewhat in the middle of the process.
From my understanding, the initial Maker run was ab initio only, we do not have ESTs or RNA-seq data to add to the pipeline. So while important, the SNAP/Augustus etc gene calls from Maker should constitute one line of evidence for our annotations, while direct alignment of homologous proteins coupled with splice-site detection (a la exonerate) should constitute another, homology-based line of evidence.
Stop me if I'm wrong.
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How come the functions of MAKER were not sufficient for your analysis?
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Thanks for the reply. As of this moment I am running genBlast and exonerate as well as the tblastn. In all of these cases, I am using the protein database of the model species as the query and my genomic sequence as the target (or database). I'll let you know how it goes.
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Originally posted by marct View PostFirst post as a user here, so please go easy on me for lack of due diligence
We have a genome assembled from Illumina data. There is a reference genome of a closely related species (same genus). I downloaded the proteins from this reference genome and sought to map them to our genome using local tblastn, as a homology-based annotation (we also have predicted transcripts from MAKER as an ab initio annotation method).
I have seen this method used in the literature, but all the method descriptions skip an important step - actually physically mapping the best tblastn hits (from whatever criteria) to the genome.
I assume there is some way to convert the blast xml output to an annotation file (GFF or similar) - one that conserves the info from the blast (especially protein name and function). I tried looking into Biopython and BioPerl but could not lay hands on the proper method of doing this.
Can someone please point me in the right direction?
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Genome Annotation Pipeline Help Required
First post as a user here, so please go easy on me for lack of due diligence
We have a genome assembled from Illumina data. There is a reference genome of a closely related species (same genus). I downloaded the proteins from this reference genome and sought to map them to our genome using local tblastn, as a homology-based annotation (we also have predicted transcripts from MAKER as an ab initio annotation method).
I have seen this method used in the literature, but all the method descriptions skip an important step - actually physically mapping the best tblastn hits (from whatever criteria) to the genome.
I assume there is some way to convert the blast xml output to an annotation file (GFF or similar) - one that conserves the info from the blast (especially protein name and function). I tried looking into Biopython and BioPerl but could not lay hands on the proper method of doing this.
Can someone please point me in the right direction?
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