Due to absence of well annotated gene boundaries, I trained a gene predictor in the absence of UTR training parameters. In such condition what can be the minimum acceptable accuracy of gene-predictor on 'gene level'?
In such case if you have exon level accuracy >80% then ~30% gene level accuracy is acceptable.
As I know, the effectors and some secretory proteins of pathogenic bacteria are involved in host interactions but I also read some articles where some groups used the whole proteome of bacteria...
11 December 2013 8,700 6 View
I'm interested in the subject of social immunity genes/proteins in insects.
09 October 2013 2,885 4 View
I have around 20,000 protein sequences of an insect predicted by a gene prediction program.
09 October 2013 8,011 4 View
I have a group of orthologous proteins as A A' A" B C D D' E F G H where all alphabets belong to different species; A A' A" and D D' are inparalogs. I want to remove the inparalogs from this group...
08 September 2013 4,586 2 View
I have several orthologous sequence clusters. I want to create a consensus phylogenetic tree by exploiting these clusters. The number of sequences per cluster varies from 2-13 and the sequence...
07 August 2013 9,626 14 View
I have pHMMs of some ortholog sequence clusters (from orthomcl). I want to add more protein sequences in these clusters. The newly added sequence in these clusters should also fulfill the...
07 August 2013 572 0 View
OrthoMCL may group out inparalogs and orthologs together in the one cluster/group. How can we identify such clusters that have "inparalogs"? How can I remove inparalogs. I only want to restrict...
06 July 2013 1,114 1 View
I need to relate the OrthoMCL clusters (that I derived from comparison of several insect proteomes) with phylogenetic tree but I am not able to understand how to proceed? I would appreciate your...
06 July 2013 3,576 3 View
I have 8000 protein sequences that I want to cluster based on similarity (not identity) and select the longest representative sequence from each cluster. I checked several tools like HiFix, SiliX,...
06 July 2013 5,750 4 View
I have an organism A which is recently sequenced. I want to find the organisms that are phylogenetically closer to organism A. I want to find the closest organism whose genome should already be...
04 May 2013 712 1 View
I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?
11 August 2024 5,138 1 View
"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....
10 August 2024 8,621 1 View
Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...
10 August 2024 8,992 0 View
Who will bear moral responsibility for the deaths of thousands of people in the event of an earthquake? Weeks and months remain before the onset of strong earthquakes that bring death to...
08 August 2024 6,134 12 View
I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...
08 August 2024 4,645 2 View
Hi, I'm currently working on a project where I need to plot the atom-projected band structure using GPAW. I've been able to calculate the band structure for my material, but I'm having trouble...
07 August 2024 269 3 View
Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...
07 August 2024 8,414 2 View
There are a huge number of methods for studying objects in space, according to the senses (and not only). Mechanical, thermal, optical, acoustic, electrical, magnetic, based on particle beams,...
06 August 2024 7,102 0 View
After immunohistochemistry of previously fixed in PFA and EtOH and then frozen 20 μm sections of zebrafish brain, DAPI staining is very weak (right) compared to the same sections stained without...
05 August 2024 9,637 2 View
I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...
05 August 2024 6,787 4 View