Questions tagged [orthologues]
Probable homologue for a given parental sequence, but may not have arisen by direct ancestry for example could have arisen indirectly for example through gene duplication
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Error with eggNOG-mapper jobs
I recently tried using eggNOG-mapper for pan-genome and core genome analysis of files from OrthoFinder, specifically the 'Orthogroup_Sequences' which contains a huge list of protein files in fasta ...
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How to use Gblocks for trimming single-copy gene sequences?
I have run OrthoFinder on a set of 11 genomes and got the results in a folder. From the output folder, I saved all the single-copy gene sequences in a single FASTA file and now wish to remove all gaps ...
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How to analyse Orthofinder results
I read this paper (Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence). We ran Orthofinder and also ...
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How to make unrooted tree for Likelihood mapping result by using IQ2-tree?
I am a biologist, and I do not fully understand the tree topology of the experimental species.
I used four-taxon set (4 sequences) to identify the Four-cluster Likelihood-Mapping by using
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Add file name to FASTA file header using SeqIO
I have several fasta files that represent the proteins from different orthogroups. However, the orthogroup that each of the proteins belongs to is not indicated within the files. I am leveraging ...
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How to annotate list of proteins with KEGG orthology groups?
I've got a list of proteins, complete with Uniprot IDs (for some of them) and gene names. I'd like to group them into orthology groups based on data from KEGG, but I have no idea how to add a column ...
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Pros and cons between genomes and transcriptomes?
What are the major differences between the use cases of a shot-gun genome and an mRNA capture transcriptome? Especially when it comes to downstream analyses such as looking for orthology, and ...
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Can ortholog genes have different names among different species?
To be specific, we have different lineages of E. coli. I wondered if the ortholog genes among them should all have the same name in all lineages or can they also have different names?
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Number of sing-copy genes identified by orthofinder is far less than BUSCO assessment?
Dear Orthofinder users and BUSCO users,
Recently, I have assessed 30 genome annotataions using BUSCO with lineage dataset ...
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How to know which ortholog database is the best for my work?
I am working on four data sets of yeast genes and one data set of mouse gene. I need the list of human orthologs of those genes. There are a lot of databases available online which is in use for this ...
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Finding orthologs [duplicate]
I am interested in finding an ortholog for a particular gene in fungi.
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Getting species from ensembl sequence id
I have downloaded some orthologues from ensembl website in fasta format. The problem is that it uses the ensembl sequence id as name for the sequences. I want to know the species name or any other ...
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Visualizing Ortholog and Paralog genes
I ran PorthoMCL but I could not find an explanation about the output format and I would like to visualise the results, maybe as a circos plot. PorthoMCL produces two output files:
Orthologs sample ...
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Finding orthologues using BLAST on the NCBI database
I'm an informatics student who has essentially zero knowledge of biology. I BLASTed my gene and have 1000s of results with very low E values. Where do I go from here if I want to find orthologues?
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