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Questions related from Shishir K Gupta
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...
12 December 2013 8,670 6 View
I'm interested in the subject of social immunity genes/proteins in insects.
10 October 2013 2,853 4 View
I have around 20,000 protein sequences of an insect predicted by a gene prediction program.
10 October 2013 7,978 4 View
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...
09 September 2013 6,203 1 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...
09 September 2013 4,511 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...
08 August 2013 9,587 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...
08 August 2013 543 0 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...
07 July 2013 3,545 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,...
07 July 2013 5,707 4 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...
07 July 2013 1,081 1 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...
05 May 2013 685 1 View
I am new to next generation sequencing (NGS). I need to format some FASTQ files. For example, I want to replace characters /1 and /2 with -1 and -2 in the files that have data like...
02 February 2013 1,407 15 View
I want to perform repeatmasking on ant genome. Ant is also included in the repeat library obtained from Repbase. The library RepeatMaskerLib.embl also contains my species. However, I also...
02 February 2013 5,108 2 View
I want to convert Sam file into Bam. I am using command $ samtools view -b -S -o bowtie.glob.bam bowtie.glob.sam, but I am getting the following error: Parse error at line 25645: invalid CIGAR...
02 February 2013 1,993 6 View
I have two signalling networks that I want to merge with "retaining network layout". I simply merged the networks with network merging utility in cytoscape however, doing this I lost the manually...
02 February 2013 7,634 3 View
I have a 47gb file to parse. The sequences are in the following format: >tscs_00041...
02 February 2013 8,742 6 View
Sometimes I wonder to see the superb images in the review articles. I am not sure weather these images are drawn by professionals or just using skills in corel draw? I really would admire your...
11 November 2012 1,410 8 View
I have a list of immune signalling proteins of Camponotus. I want to identify the isoforms of these proteins. Is it possible to get the isoforms by searching the corresponding genes in NCBI? Is...
10 October 2012 4,189 1 View
Among the multiple entries of sequences for same protein of a specific organism in any database, which entry should be used for further task? Is there is any specific criteria to select such...
09 September 2012 7,921 4 View
In a signaling network, if the protein A is activating the complex (XYZ) then in such a case how should we show this relationship (for further modeling purpose)? Is it like this: A ---->X , A...
08 August 2012 6,618 4 View
Is it good to change research direction? If yes, then how can the change in research direction help advance scientific careers?
08 August 2012 1,126 1 View
I have 4 networks in Biopax 3 format. I want to integrate my networks. Could anyone suggest tools or methods for such integration?
08 August 2012 8,640 5 View
I want to know the list of phylogenetically close organisms of C. floridanus. How can I access this information. (C. floridanus is sequenced recently).
07 July 2012 9,338 30 View
ab initio methods for protein structure prediction are limited to model around 120 AA length protein. What is the specific reason for this limitation? I would appreciate your answers.
03 March 2012 983 1 View
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01 January 2012 6,955 17 View
I recently constructed a full-length model of protein using multiple templates. Is there occurs any possible impact on inhibitor binding at active site by using either a truncated model (model of...
10 October 2011 6,768 0 View
