Eszter Ari

6 Questions 8 Answers 0 Followers

Questions related from Eszter Ari

Is there a way to search for unannotated genes in metagenomic sequences e.g. on MG-RAST using a sequence similarity search algorithm??

Please suggest a website, API, or other solutions to sequence similarity searches on many (all available) metagenomic libraries without downloading the metagenomic reads or assemblies. Thank you

09 June 2023 6,841 2 View

What cut-off should we use when applying BUSCO to Escherichia coli (Bacteria) genome assemblies?

We would like to analyse thousands of E. coli genomes and identify orthologous genes. Before this we would like to filter the bad quality genomes by BUSCO (https://busco.ezlab.org/). What % of...

16 November 2020 5,332 3 View

How to find the nearest tips on a phylogenetic tree?

I have a large phylogenetic tree and a list of tip names for which I would like to know their closest relatives (based on the tree). The tree has polytomic nodes as well. Can you help me to solve...

15 June 2020 1,429 0 View

How to reconstruct the phylogeny of thousands of E. coli strains?

Dear Community, I would like to reconstruct the phylogeny of 16,000 E. coli strains based on their genome sequences. What do you think about the following concept? 1. ORF prediction in all...

17 September 2019 5,213 9 View

Is there a solution to do Generalized Linear Model based differential expression analysis (RNA-Seq, not pairwise comparison) of Pathways (not genes)?

The canonical way is to find the differentially expressed genes and than do gene set enrichment analysis. But is there a solution to include the pathway information before calculating differential...

16 May 2016 6,009 3 View

Why are genomic (non-mitochondrial) tRNAs not annotated in the human genome?

At least I cannot find them on Ensembl or USCS. I know some specific databases for tRNAs like tRNAdb and GtRNAdb. But I am really suprised that there are no tRNAs in the reference human genome...

18 September 2015 2,340 1 View