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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...
12 December 2017 3,827 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...
10 October 2017 8,795 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...
06 June 2017 6,680 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...
03 March 2017 9,516 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...
02 February 2017 2,256 3 View
Lets see an example. The reaction R00344 is mentioned as irrversible in KEGG
07 July 2016 4,766 3 View
PS: I have single time point gene expression data for around half of the gene in the signaling network.
05 May 2016 3,018 2 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...
05 May 2016 7,560 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...
04 April 2016 10,051 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...
04 April 2016 3,310 5 View
I have some mixed genome sequence data of an insect. The insect contains 1 known and probable some unknown symbionts. Could someone please suggest me how can I identify the unknown symbionts if...
11 November 2015 9,097 1 View
Is the apical and basal epithelium both have receptors? I know there are several receptor that localize on apical surface but are all the receptors co-localize on apical and basal side of gut...
08 August 2015 1,758 1 View
Several organism at NCBI have sequenced genome but no predictions of proteins. For example Caenorhabditis japonica genome is there but the NCBI ftp also lacks its proteome. What should I do to get...
08 August 2015 9,441 4 View
Could someone suggest me what should be the test set for performing Fisher's Exact Test in blast2GO?
08 August 2015 6,218 3 View
I am not sure if it is good solution to replace such characters in the alignment with gap. What you do to deal with such undetermined amino acids/ nucleotides?
04 April 2015 2,977 9 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...
04 April 2015 9,046 12 View
I have a large concatenated protein multiple sequence alignment. One of the species have many undetermined 'X' amino acid. Such column will probably not add much phylogenetic signal so I want to...
04 April 2015 4,377 23 View
I want a consensus annotation for group of orthologous protein. I know Interpro, KOG/COG, Blast2Go are the nice option to do functional annotation but here I do not always have the similar...
02 February 2015 4,939 3 View
I want to check the whether my proteins of interest are positively or negatively selected but the orthogous proteins groups I have are like orthologous group - A A' B C D D' D" E ...
02 February 2015 8,492 7 View
I have ~50 protein alignment files. Each file have single copy ortholog of five bacteria. I extracted the protein sequence from NCBI and species I used are sequenced. 1- For the positive selection...
12 December 2014 9,678 12 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...
12 December 2014 378 11 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...
11 November 2014 2,922 13 View
I am surprised with the zdock results for my peptide and 3 different receptors. I removed the polar hydrogens added Charmm forcefield and performed docking with zdock six degree of freedom and...
11 November 2014 4,154 6 View
These results are the part of two-channel microarray experiments- Each gene was in triplicate on the array and each sample was hybridized with a flip-dye replicate in order to account for labeling...
10 October 2014 8,374 4 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 ...
10 October 2014 7,686 10 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?
10 October 2014 1,229 6 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...
09 September 2014 357 3 View
I want to add a subcellular localization filter on my predicted host-pathogen interactome. Could someone please tell me what should be the localization of protein interaction if one partner is...
09 September 2014 5,482 3 View
I realized that some researchers present the same 'poster' in different conferences. I wonder whether it is scientific misconduct?
09 September 2014 9,789 0 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...
09 September 2014 4,187 3 View
I have cluster of protein sequences form my fungi, associated with EC numbers and reactions. I want to create draft metabolic reconstruction. Are there any automated tools which can be used to...
07 July 2014 6,954 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...
06 June 2014 7,698 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.
05 May 2014 295 2 View
I know several researchers who like to write during the execution of work. In last two years I have generated plenty of data but nothing on paper. When I start to compile, I feel like I lost some...
05 May 2014 1,105 7 View
I have thousands of blast output XML files that want to join. For tabular blast output it is very handy. Could someone suggest the way to join all blast output files?
04 April 2014 1,735 2 View
Is it possible to remove the sequences of particular species from locally downloaded nr db of NCBI?
04 April 2014 976 4 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...
04 April 2014 2,772 7 View
Besides gene essentiality and non homology with human proteins.
04 April 2014 2,591 2 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?
04 April 2014 9,377 7 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...
04 April 2014 463 3 View
How do other researchers manage their time? I always feel that I have to compromise a lot with my personal life for doing research. I want to do many things in my personal life but always have...
04 April 2014 9,099 45 View
Kegg ftp has not been freely available for a long time. Does someone have any older version of the kegg pathways and protein database?
04 April 2014 8,990 3 View
Which tool performs better for domain detections? What is your experience with these two?
03 March 2014 2,561 4 View
I have around 15,000 protein sequences which are product of newly re-annotated genome. The sequences looks...
03 March 2014 2,855 4 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...
02 February 2014 4,934 6 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?
02 February 2014 5,398 2 View
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?
02 February 2014 7,058 0 View
Could anyone tell me how to get a Rosetta License?
07 July 2012 376 1 View
07 July 2012 1,576 1 View
It is a pity for a bioinformatician that his work is often not appreciated by Wet-Lab researchers. So how a in silico researcher can get a position in life science graduate school? I would...
02 February 2012 3,695 13 View
I am looking for some good question to ask as think it also affects the position. I would appreciate your suggestions.
02 February 2012 9,191 3 View
