Hello,
I am trying to see the location of genes and their neighbors (what sort of functions they are doing) in a genome. So, could anyone recommend any good browser? Any suggestions would be helpful.
Thanks!
-Spandan
Artemis is One of the useful genome browser you can find helpful.
A list of Genome Browser softwares is provided in below link.
I recommend the IGV (http://www.broadinstitute.org/igv/home). It has a detail tutorial and supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. If you have installed JAVA, you can easily start from using JAVA Web Start without any install process.
Synteny Analysis in Ensembl provides a list of upto 15 upstream and downstream genes for a query gene based on syntenic regions between different species.
Try UGENE. It's open-source and free. It has a polyfunctional tool. http://ugene.unipro.ru/
The WashU Epigenome Browser have a cool feature called 'Juxtaposition', which brings user-defined genes/regions together for easy comparison view. Supporting flexible extension of regions/genes.
For OP's question, simply right click on any gene track, choose 'Juxtapose', you will see all genes would be placed near each other :)
Persephone Software is working on the web version of their genome browser. It is free, though does not yet have all the features of their paid enterprise desktop version. It is very fast and is tailored to show several genomes at once, linking syntenic chromosomes. Check it out at http://web.persephonesoft.com
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
Another biostar post about it here: What tools/libraries do you use to visualize genomic feature data?