Tweet
Does someone know any program for in silico enzyme digestion. I am a web lab scientist , need to do a computational simulation for whole genome enzyme digestion. I need a program which has the input option for genome, enzyme, the resulting fragment size range, also whether the fragment is unique. The output file are something like the Bed file like format with chr, start, end, and fragment size etc. It will be great that it can also give a distribution plot for the fragment. Thanks a lot!!!! I will be really appreciate.
-
-
This paper has a program for it but I don't know if it is available:
Zhou et al. J of Bacteriology 2004
-
There is an instrument!
Hi -
The reference cited is the basis of an instrument that does this type of mapping made by OpGen. See OpGen.comComment
-
Hi sunsnow86,
Did you manage to find thein-silico digestion software you were looking for? I'm looking for the same now.Comment
-
Counting RE site in bigger genome
Dear sunsnow86 and fastidiousme,
Did you find somw tool/scripts to estimate restriction enzyme sites in bigger genomes? I am also looking for the same.
Regards,
SComment
-
Probably multiple tools out there, but it is also a good project for a beginning bioinformatics student. Without excessive bells-and-whistles, should be about a page of code in any high-level language with good bioinformatics library support (e.g. Perl, Python, Java)Comment
-
At the intersection of cytogenetics and genomics lies the exciting field of cytogenomics. It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. By integrating cytogenetic techniques with genomic analysis, researchers can effectively investigate chromosomal abnormalities related to diseases, particularly...09-26-2023, 06:26 AM -
Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...09-07-2023, 11:15 PM -
Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.
Whole Transcriptome RNA-seq
Whole transcriptome sequencing...08-31-2023, 11:07 AM
Comment