Does anyone know if it's possible to predict, from a genomic sequence, the gene structure ? And which software is available for download?

More Humberto Contreras-Cornejo's questions See All

How can the phylogenetic signal be measured or detected using mitochondrial DNA sequences?

I would like to know which software is the most commonly used or recommended for this analysis. Best regards, Cristian

29 March 2017 2,899 1 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

How to calculate average trend in maximum annual NDVI from MODIS?

I am wanting to calculate the average trend in maximum annual NDVI in Iceland from 2010-2020 using MODIS MYD13Q1 V6. How would I do this? I have currently inserted the NDVI bands from the MODIS...

02 March 2021 752 2 View

Why does two different bioinformatics tools for the same proteins show different subcellular localizations?

During a computational analysis, I found that for a protein of a plant, two different subcellular localizations are seen using CELLO and WoLF PSORT. For example, in CELLO, it identified the...

01 March 2021 6,729 2 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

Genome-wide gene identification protocol ?

Is there any book chapter/book, webpage or research article available to understand genome-wide gene identification?

28 February 2021 8,095 1 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

I have need of XRD graph analysis software for phase identification. Can you please provide links for software tools which can be downloaded?

i am trying to download x'pert high score software, but can't download it. please do suggest software for phase analysis

24 February 2021 5,687 4 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Ravi Kant Upadhyay

You can use GeneMark™ - Free gene prediction software, and prediction of probable genes by Fourier analysis of genomic sequences si also possible. GeneScan can locate coding open reading frames and exonic regions in genomic sequences.

Harlan R Barker

Are you looking for a specific gene that you know exists in other species? If so then you can use orthologs of your suspected gene and the Exonerate program. The results of this will be superior to any de-novo prediction software if your case fits the requirements of the first sentence.

https://www.ebi.ac.uk/~guy/exonerate/