Some gene prediction tools such as FragGeneScan use a 6-periodic HMM (di-codon) to represent the coding region.
Why do these tools choose a 6-periodic...
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Why do some gene prediction tools represent the coding region in HMM with 6 states?
Last edited by Mia Blige; 05-09-2021, 08:24 AM. -
Problem with UCSC GTF files?
Hi,
I would like to ask for some opinion and advice related to the different available GTF-file sources for annotated genes.(mm10, but... -
Problem with UCSC GTF files??
Hi,
I would like to ask for some opinion and advice related to the different available GTF-file sources for annotated genes.(mm10, but... -
correlate taxa with the gene function
Hi,
I am doing a project on metatranscriptomics. I followed the Trinity tutorial for doing differential gene expression and annotations.... -
Consensus tree with missing data
Hi,
I have a phylogenetic trees built from alignments of sequences of a set of genes (1 gene per tree), where the final nodes are the individual... -
How do you extract regions of interest when you have massive exome data?
Hi everyone,
I am new to bioinformatics and I have been having trouble with exome data. I've practised using standalone BLAST+ and I've... -
Please I need some help on this.
Please I'm having problems with weblem 5-6 and 5-11 on growth hormones:
https://global.oup.com/uk/orc/xediti...f4exe/student/... -
Expression profiles probe id meaning?
Hello,
What is difference between different probe in the gene expression profiles?
e.g. Gene: IGF1
Probe ID: 211577_s_at,... -
Fetching minimal \ maximal transcription position per gene for UCSC\RefSeq
Hi,
I'm working with two gene tables (the UCSC knowngene table and the RefSeq refGene table) - the user of my program will choose which... -
Expressed genes vs Expressed transcripts
I analyzed differential gene expression using Cuffdiff, but the number of genes expressed is smaller than transcripts expressed. Anyone can explain this?... -
HTSeq exon counts to gene level
Hi,
I'm working with drosophila melanogaster RNA-Seq data and at least one of my genes of interest is overlapping an other gene so I used... -
Pipeline suggestions for gene detection
Hi everybody!
I've been searching this question through the internet and forum but I didn't find an answer.
I'm working... -
Pre-written tools for gene burden tests?
Hello everyone,
I am writing to ask about tools that perform gene burden tests that are already written and will work on a VCF file.... -
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... -
Is there a good protocol for annotating genes and exons?
Hi,
I am running an analysis on RNASeq data, and have already detected some (putatively) novel exons and genes. What I now need to do is...
