Questions tagged [functional-annotation]
The functional-annotation tag has no usage guidance.
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Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka
I am trying to run the Prokka annotation tool on my linux machine and have installed Barrnap and added it to $PATH and given the folder chmod 777 permission. However, when running Prokka, it gives the ...
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I have a partially described gene from a plant, which tool may I use for predicting regolatory and UTRs sequences from a single DNA fragment?
I have a partially described gene from a plant with CDS and 3'UTR described but no 5'UTR; if I know the locus and upstream and downstream regions, is there a tool I can use for predicting regulatory ...
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Bulk protein annotation with Prokka
Can prokka be used to annotate a set of protein sequences (so bulk protein annotation), or does it require an entire genome for the annotation?
I've been looking through the documentation but haven't ...
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MAGs transcriptomics pipeline question
I have currently a following problem. I have a one sample that I did my metagenomics on (Illumina shotgun + nanopore) and have recovered some high quality MAGs. I also did a metatranscriptomics on the ...
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Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?
I am currently working on a network pharmacology project where I am supposed to find out the possible diseases our drug might have an effect on. I am not a bioinformatics student, so my knowledge in ...
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Gene Ontology equivalent - higher specificity?
I've recently discovered OrthoVenn2, which I'm using to compare proteomes and extract likely clade-specific genes. I'm enjoying software, and one of the things it offers is a breakdown of protein ...
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Differential Expression
I have genes differentially expressed between two groups (case and control). I would like to annotate them by classifying them according to their biological functions.
I work on parasites of ...
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SwissProt Proteins into my Jbrowser
How is it possible to get the SwissProt Proteins into my Jbrowser in the same way like shown below?
Thank you in advance,
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How to get the GO information for all the human genes?
I would like to retrieve a list of all the human genes and their proteins’ functional classification.
The Gene type attribute on ensembl.org is not specific ...
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Why are my genes filtered for Gene Ontology term enrichment?
When I enter a list of gene names into common gene ontology (GO) term enricher (e.g. MsigDB or ToppGene) only a small fraction of genes is actually used for the enrichment:
I am struggling to ...
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where to find pathogenicity metadata for E.coli genomes
I have a list of about 900 E.coli genome ids (Genbank plus NCTC ids), e.g.:
...
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Compare functional enrichment between genelists
I want to compare the results from functional enrichment (e.g GO term enrichment generated by gProfileR) between two gene lists. The idea is to see if these gene lists are enriched in the same terms ...
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SnpEff gene annotation with @ such as PCDHB@
I'm using snpEff to annotate some VCFs and getting some spurious annotations that don't have transcript ids. Some of these annotations have a gene name followed by ampersand such as PCDHB@ and I'm not ...
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Downloading full search results from BlastKOALA?
I have just started using BlastKOALA KEGG which has been useful in annotating (aminoacid) sequences. This is their website: https://www.kegg.jp/blastkoala/
When you get results, there are links for ...
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RNA seq fasta file annotation from alignment to reference matches
I've got a fasta file with some RNA seq data and another csv file with the output from plast where I've aligned it to a reference using plastn. I'm struggling with figuring out a command to append my ...
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How to run SIFTER stand-alone version
I have downloaded the core version of SIFTER. I am not able to run it because I get the following error.
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Find specific functional genes from a list?
I have compiled a list of genes that are distinct from 2 different conditions.
From this list (of about 600 human genes), I want to find out if any of the genes in this list have acetyl transferase ...
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Why does RATT create a directory with chromosome sequences and how can I stop it?
I have run RATT to transfer the annotation from a reference strain to another strain. For this, I have run:
...
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Problem installing RATT
I have followed the steps here to install RATT, i.e.:
svn co "https://svn.code.sf.net/p/ratt/code/" ratt-code
However, when I check my installation by running '$...
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Is there anything similar to GSEA for locus-based (instead of of gene-based) data?
As the question states, I am interested in an analysis similar to Gene Set Enrichment Analysis (ranked gene sets) but focused on locus-level data instead of genes.
To explain in greater detail: I ...
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