I have some protein families. I want to create a local HMMER like webserver/tool and implement hmmsearch in it. Please suggest me how can I implement this?
I have 12 species from same genus. For supermatrix approach we generally use the multiple sequence alignment single copy orthologs sequences then concatenate them and remove the badly aligned...
11 December 2017 3,868 4 View
I read several papers where researchers use several strains of same species for analysis of recombination or selection pressure however there are few papers in which researchers use the multiple...
09 October 2017 8,848 4 View
The ortholog groups of 5 species proteins look like: Group1: sp1 sp2 sp3 sp4 sp5 Group2: sp1 sp2_seq1 sp2_seq2 sp3 sp4_seq1 sp4_seq2 sp5 (sp is for species here) As here one can see the Group1...
05 June 2017 6,710 1 View
I need to evaluate the accuracy of predicted interactome of an insect species which I constructed by interolog method. I read that I can use ROCR package for it. I got a gold standard positive PPI...
02 March 2017 9,554 1 View
I need to run codeml for ortholog clusters from different related genus. Do I need to generate a species tree for it that I can use for all the clusters or I need to generate gene tree for all the...
01 February 2017 2,304 3 View
Lets see an example. The reaction R00344 is mentioned as irrversible in KEGG
06 July 2016 4,805 3 View
In principle, this questions is like quora flavor. Here, I am asking this question for a bioinformatician perspective but surely would like to know you opinion about the other journals that are...
04 May 2016 7,593 2 View
PS: I have single time point gene expression data for around half of the gene in the signaling network.
04 May 2016 3,055 2 View
I have created a PPI network, now I want to compare it with random networks. I can generate the random network. In general, I am interested in the comparision plots of (i) degree vs betweenness...
03 April 2016 10,079 4 View
I understand the over-representation of GO term in FDR test against reference gene sets but the under-representation seems confusing. My test set is infection induced differentially expressed...
03 April 2016 3,359 5 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
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
Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...
05 August 2024 6,247 3 View
In the case of a wound l recurrence after radical breast cancer and sentinel lymph node biopsy. Are the sentinel lymph node procedure recommended? If no axillary lymph node dissection was not...
05 August 2024 8,056 1 View
Regarding a model for simulating battery charge and discharge, what do you consider to be high fidelity? What is the acceptable percentage of error (regardless of the metric)? Could you suggest...
03 August 2024 5,358 0 View
Hi RG family. My team and I are working on some SCOPUS publications and we need co-authors who are willing and capable of undertaking both qualitative and quantitative-based studies. The scope...
02 August 2024 7,843 0 View