25 Questions 29 Answers 0 Followers
Questions related from Ashmit Singh
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...
30 December 2017 1,539 3 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...
08 June 2017 4,228 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...
08 March 2017 6,227 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...
28 February 2017 2,669 3 View
PS: I have single time point gene expression data for around half of the gene in the signaling network.
31 May 2016 4,856 2 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...
28 April 2016 1,042 5 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...
19 April 2016 1,971 3 View
I have orthologous protein clusters from four metazoan. I dont't know the corresponding genome regions from where these proteins are derived. I can extract that with blat (if needed). I want to...
25 April 2015 567 11 View
I am constructing an interolog based host-pathogen protein-protein interaction network. As per I know the secretory, extracellular and membrane proteins of gram negative bacteria can interact with...
29 December 2014 5,316 10 View
I have >1500 sequence clusters, all have 7 orthologous sequences from different species. When I look at multiple sequence alignments of some of these sequence clusters, I found some of the...
23 November 2014 1,231 15 View
I annotated the Aspergillus proteins by Kaas server and Kegg however, I am not confirmed whether the pathway annotation is correct. For example protein XP_752857.1 (AFUA_1G14880) is annotated with...
02 November 2014 2,891 12 View
I want to select 10 different symbiotic bacteria for comparative analysis of different protein family members. My question is how can I decide whether the functional and structural annotation of ...
09 October 2014 1,240 9 View
It is reported that inparalogs generated by gene duplications subsequent to speciation exhibit similar functions. Do they also share similar PPIs and similar signaling interactions?
03 October 2014 5,542 4 View
I want to create a infection model of JNK pathway but I only have data of single time expression calculated by Cuffdiff. Out of around 12 proteins in the pathway if I map the significant fold...
18 September 2014 9,146 3 View
I have a large protein-protein interaction based on orthology with experimental PPIs. I want to transform my network to signalling pathways. The NetSearch algorithm can be applied for this but I...
13 September 2014 5,080 3 View
I have a set of proteins from organism X. I want to estimate the conservancy of these proteins across 9 other organisms. I did the orthology search but it gives the counts weather the protein...
28 June 2014 5,068 3 View
I have a large list of EC-numbers. I want to find out the reactions associated with them. I could not find the way to retrieve all together from Biosyc.
21 May 2014 8,637 2 View
I know the computations by breaking the files and parallelize it in SGE or SLURM. I want to use whole computation power (20 node, 80 cores) for a single job without breaking it. If I just submit...
25 April 2014 9,340 3 View
I have 1000 pdb files. I want add polar hydrogen in the files. Could someone suggest any command line program to add polar hydrogens to pdb files?
17 April 2014 5,844 7 View
Besides gene essentiality and non homology with human proteins.
13 April 2014 7,364 3 View
Could someone suggest the method to prioritize proteins as drug targets? I have 200 protein targets that I want to prioritize based on their features and properties like molecular weight,...
12 April 2014 8,912 1 View
My docking results on the same grid and the same machine are different. For the same grid both the Windows and Linux systems also give different a docking energy. I read that the system generates...
07 April 2014 1,108 6 View
Which tool performs better for domain detections? What is your experience with these two?
28 March 2014 2,580 3 View
I have my own dataset of proteins. I want to use this dataset as a blast database. I know it is possible in offline blast but my question is is if there is any online blast utility where we can...
18 February 2014 8,485 5 View
The protein interaction network created directly from literature (not using any template network or omics data) will be under Top down or Bottom up approach?
12 February 2014 4,290 1 View
