Hi,
I'm want to annotate a big, complex eukaryotic genome from non-model using GeneMark 4.69 gene prediction.
I want to train...
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training GeneMark for gene prediction
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Downloading data from ncbi
Hello
I've been trying to get the hang of NCBI's esearch suite as I want to download their gene summary paragraphs. Would anyone be able to clarify...Last edited by Cannon; 01-13-2022, 04:30 PM. -
Gene annotation with Augustus
Hello all,
I am doing structural gene annotation and using augustus as a tool. While it works quite nicely on most of the cases it shows... -
Uniprot IDs for a whole genome
Hallo,
I have extracted a population bin from a metagenome. I have also uploaded the same to the genebank. But according to their rule... -
koushik started a topic Pairwise comparison of genes which are common between two different species in fungiin GeneralPairwise comparison of genes which are common between two different species in fungi
After completing the genome annotation of two different entomopathogenic fungi species namely Beauveria bassiana and Metarhizium anisopliae. How can we... -
TCGA gene annotation conversion for RNA-seq datasets
Dear all,
I downloaded some RNA-seq datasets from TCGA but I am not able to convert the gene ids to the current ensembl annotation release.... -
tophat gene information
Hi all!
I used tophat2 with the option -G in order to give the gtf file but the output reported the chromosome coordinate. Why? What did I get... -
Identifying genes from contigs
Hello All,
I have got a fasta file containing a list of contigs which were obtained through transcriptome analysis. Now, I want to find... -
How to use Gene Annotation Model in Tophat2
I'm using Galaxy to analyze RNAseq results for differential gene expression in Drosophila mel.
In tophat2, it says that I can supply... -
BioGyan: Search Mine Annotate
BioGyan (http://www.biogyan.com/) is a comprehensive search tool specially designed for biologists, enabling search, annotation and ranking of scientific... -
Finding a gene of interest in a scaffold
Dear all,
I'm having my first go with working with a newly sequenced genome. I have a bacterial genome sequence in scaffolds assembled... -
How to annotate genes from gene prediction
Hi,
For a completly novel genome I used a gene prediction software called SNAP (http://korflab.ucdavis.edu/software.html) and it provided me a GFF...Last edited by mictadlo; 09-17-2013, 06:00 PM. -
Gene Set Enrichment Analysis
Hi all,
I have used the cummeRbund function findSimilar() to find the 10 most similar genes to the differentially expressed genes I identified... -
Functional annotation of OrthoMCL groups?
One of the cons of OrthoMCL is "OrthoMCL groups do not have function annotations". Could someone suggest me how to annotate the OrthoMCL gr... -
JIGSAW gene prediction combiner - use for prokaryotes?!
Hi, I have a recently assembled bacterial genome. It consists of a a couple dozens scaffolds, and I have put them through three gene prediction methods:...
