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Questions related to Bioinformatic Tools
1. There are several database containing nifH sequences like fungene (19500 seq), arb database (32,954 seq), zehr (72000 seq) and farnelid (5,00,000 seq). what is the difference between these...
02 February 2020 706 3 View
Prediction of enzymatic activity based on common genetic variation.
02 February 2020 8,632 2 View
I'm relatively new to bioinformatics tools and need to look at biosynthetic gene clusters, someone suggested using antiSMASH but I have no experience of this software. Can anyone suggest any tips...
02 February 2020 6,820 2 View
I want to pulldown all ubiquitinated proteins in the proteome and analyse them using mass spec. Are there any recommended kits for pulling down Ub tagged proteins for further mass spec analysis?...
31 January 2020 3,752 0 View
Recording of European flat oyster Ostrea edulis in adjacent coastal waters of Colombo Port can be considered to be rather surprising, and I wonder if this was mistaken for a local oyster that...
18 January 2020 9,910 4 View
As mentioned above, I am having trouble with my subcellular fractionation of 4T1 cells. For my cytoplasmic lysis buffer, I am using 1% TritonX-100 Lysis buffer (20mM HEPES, 50mM NaCl, 1.5mM...
06 January 2020 9,804 2 View
Dear all, I am analyzing WGS sequences of Enterobacteriaceae. However, I do not have any experience in software based on OSX or Linux. Could you recommend me user-friendly software (better free)...
01 January 2020 9,733 2 View
I am looking for a tool that can help in identifying binding region in the nucleotide sequence of a gene for transcription factors or help us to identify the transcription factors that can/may...
01 January 2020 2,408 3 View
Hello, I have a list of genomic coordinates from differentially methylation regions and a I need to extract from them a list of genes, and I don't want do look one region by one. Is there a R...
01 January 2020 3,337 4 View
Which book should I read to understand bioinformatics from the very beginning?
23 December 2019 7,295 24 View
hi, i am seeking for a tool or method for making protein prediction for a rare sequence, the protein has 256 residues and doesn't have any template which aligns, also there are 34 Gly, 10 Pro...
12 December 2019 8,061 5 View
I used MEGA7 to determine the best substitution model and the SM with the lowest BIC value is the LG substitution model. However, I can't find LG when I want to make a maximum likelihood tree of...
12 December 2019 5,153 1 View
Do you know any database for searching about endemic species, their genomes, differences, DNA barcodes etc.?
28 November 2019 285 3 View
Wolbachia is an endosymbiont bacteria in some filarial nematodes. It codes for some specific enzymes which regulate specific metabolic pathways. Here what I want to know is how to detect nuwts to...
11 November 2019 775 1 View
I wanted to detect the terpene synthase gene (TPS) in Eleusine coracana (Finger millet) plant, whose genome size is 1195.99 Mb, by the bioinformatics tool as it is not reported yet. The problem...
11 November 2019 3,335 1 View
I have a unknown transcript and want to find out its CDS region translated into protein. Kindly help me which bioinformatics tools will be helpful in finding this information.
11 November 2019 9,587 4 View
I did some in vivo imaging using a V5 epitope-tagged protein in C. elegans germline. V5 tag works really well for Immunohistochemistry and generally gives less background. But now I am looking...
07 November 2019 8,366 0 View
04 November 2019 1,789 3 View
Hello, I am trying to find a bioinformatic tool to use on multiple sequences and get a devision into categories , until now I have used T-COFFEE score to devide to catagories., for example, a...
29 October 2019 6,034 3 View
The OVCAR-3 medium suggested by ATCC is RPMI-1640 with 0.01 mg/ml bovine insulin and 20% FBS. I would like to replace bovine insulin for human recombinant insulin. Has anyone tried this? Thanks in...
16 October 2019 8,147 0 View
I am doing ATAC-seq with a new kit form Nextera which does not include Tn5. I bought separately Tn5, but it still does not work. I also used EPM from the new kit with indexes from Illumina, and...
15 October 2019 9,446 0 View
Dear Experts, I was trying to use REVIGO ( http://revigo.irb.hr/ ) for GO visualization. But I have more than one GO terms associated with a specific gene, which is expected and possible. REVIGO...
10 October 2019 1,015 1 View
I used VEGA, DANISH as well as PASS prediction to check ADMET properties. but any better suggestion?????
10 October 2019 7,885 4 View
10 October 2019 5,696 3 View