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Questions related to Bioinformatic Tools
Which bioinformatics tool such as swiss regulome portal is best for finding transcription factor of a gene?
10 October 2018 8,981 3 View
Hello, everyone. I'd like to know if anybody has an executable file of Kalign tool for Windows, since it is, nativally, for Unix. Thanks!
10 October 2018 3,101 6 View
Hello everyone! My field is genetics, but i'm interested in learning statistical genomics and bioinformatics as well. For self-educational purposes, i want to reproduce PennCNV software (for...
10 October 2018 4,252 0 View
I am not a specialist in genome annotation procedures. I found a good review "A beginner's guide to eukariotic genome annotation" written by M.Yandell and D. Ence in 2012. They mention that...
10 October 2018 4,981 5 View
I have used Albacore (v2.3.3) to basecall my minION data locally on my machine. Within the produced "workspace" directory albacore is outputing two folders ("pass" and "fail") based on the qscore...
10 October 2018 3,494 5 View
Dear all, Now a days there are too many bioinformatic tools and sftwares freely available on the net like SIFT and Polyphen. These tools are able to predict the effect of specific varaiant on...
10 October 2018 677 2 View
Hi, everyone. I recently analyzed a set of RNA-seq data. Based on the fold change rank, a batch of ncRNA shows as top up-regulated in RNA-seq data. I am new to RNA-seq analysis. Is it normal in...
09 October 2018 765 2 View
I determined the Ka/Ks ratio for the matK gene. The MAFFT alignment showed 6 SNPs which were non-synonyms and covert six amino acid. The whole size of the matK gene has 1509. I extract alignment...
29 September 2018 2,144 1 View
I'm looking at the gene sequences of a pair of enzymes and related processing proteins and am trying to figure out whether they are in the same operon, and where the operon begins and ends.
09 September 2018 8,597 8 View
I have docked two interacting proteins and get a pdb file, now I want to know the prediction of binding residue sites by this docked pdb file. Please suggest me some bioinformatic tools for this.
09 September 2018 1,663 5 View
Hi, I have an amplicon of 1.6kb and I have sequenced it using forward and reverse primer. Now, I have to trim both the sequences and assemble those into one contiguous sequence. My goal is to...
09 September 2018 1,238 5 View
Hi! Everyone. I am looking for a good commercial software/product for homology modelling in order to generate protein structures. Currently, i'm working on bacterial protein. Is there any...
09 September 2018 1,924 10 View
I am working on Secondary metabolites, I have identified the gene clusters using the AntiSmash bioinformatics tools, now I am interested to find the Silent Biosynthetic gene cluster. can we...
09 September 2018 6,959 7 View
If I have a .gff file or a .faa file, how can I use this information to understand what the average length of all the sequences are. Or is there a program to visualize the distribution of...
09 September 2018 7,303 3 View
Suppose within body fluid (e.g., blood) there are exosomes with specific marker protein to be detected. I want to know what type of molecule might have the possibility to interacts with the...
09 September 2018 6,010 0 View
Hello, I’m planning on learning drug design and molecular docking. I want to know if there is any book that could help me in the process. I have already found these books: 1- Computer-Aided Drug...
09 September 2018 3,124 4 View
04 September 2018 3,015 6 View
04 September 2018 8,518 6 View
Hi there, I need to import a DNA molecule into a crystallographic pdb file containing a viral capsid. Furthermore, I want to add some ion molecule surrounding the viral structure. Is there any...
20 August 2018 4,617 4 View
Can anyone recommend any proven bioinformatic tools to analyse a DNA sequence, and output predictions for transcription factor binding sites? Many thanks!
08 August 2018 1,723 3 View
08 August 2018 8,602 5 View
I am collectiing targets informations of a set of compounds by using the ChEMBL databases. And I notice in the ChEMBL Target Search Results website, there is a "bioactivities" column. The value...
08 August 2018 4,014 2 View
Tropical Plant Pathology is a journal which recommend me to use the given style for referencing so how to recognize in EndNote that which type of style this is ? Reis RF, Goes A, Timmer LW...
08 August 2018 8,254 3 View
I have a gene, let's say p300, and I have a list of genes that are co-expressed with it. I want to find which of these genes have the most similar function to p300. What would be the best tool for...
23 July 2018 5,678 3 View