Questions tagged [functional-annotation]

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How to parse hmmsearch output?

I did hmmsearch with --notextw and --domtblout and I see several results for ids, I want to ...
bobr's user avatar
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-1 votes
1 answer
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Where can you download functional domain labels of the human genome?

I'm visualizing where mutations occur in a gene, and would like to add functional domains to the plots. I have some trouble locating sources to download data on functional domains. The dataset should ...
Sofie's user avatar
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PANTHER FUNCTIONAL CLASSIFICATION in R

Does anyone know of a way to programmatically get panther protein class terms and IDs for a gene list, in a way that the classification structure is preserved (PARENT CLASS + CHILD CLASS)? i.e. For a ...
ricardo3889's user avatar
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Exporting Panther functional classification of gene list

After inputting a list of gene and running an analysis in https://www.pantherdb.org/ (such as "functional classification"), I get a result table that is limited by an X number of entries ...
ricardo3889's user avatar
3 votes
1 answer
207 views

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 ...
Harish Prabhakar's user avatar
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1 answer
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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 ...
user16622's user avatar
1 vote
1 answer
26 views

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 ...
Isa Wilkie's user avatar
2 votes
0 answers
30 views

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 ...
Avamys's user avatar
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1 vote
1 answer
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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 ...
Gee3's user avatar
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1 vote
0 answers
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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 ...
Laura's user avatar
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1 vote
1 answer
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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 ...
Diango's user avatar
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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,
user977828's user avatar
2 votes
0 answers
289 views

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 ...
0x90's user avatar
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0 votes
1 answer
48 views

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 ...
Tapper's user avatar
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2 votes
1 answer
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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.: ...
719016's user avatar
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1 vote
1 answer
218 views

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 ...
plat's user avatar
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1 vote
1 answer
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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 ...
111's user avatar
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1 vote
0 answers
206 views

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 ...
Scientist's user avatar
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2 votes
1 answer
70 views

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 ...
ladle-mocha-17's user avatar
1 vote
0 answers
40 views

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. ...
mpourreza's user avatar
1 vote
1 answer
82 views

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 ...
Dan Lu's user avatar
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1 vote
1 answer
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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: ...
Biomagician's user avatar
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2 votes
1 answer
108 views

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 '$...
Biomagician's user avatar
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3 votes
2 answers
78 views

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 ...
Reilstein's user avatar
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