Caution: fastacmd is not case-sensitive

I have used the NCBI BLAST toolkit to extract sequences from a fasta-formatted file. Briefly, a fasta file can be formatted with the program formatdb and then sequences can be extracted from the database using fastacmd. Note, fastacmd is not case-sensitive, which means that one can use the following two... Read more »
January 19, 2017

How to add Chinese Pinyin (拼音) in Microsoft Word 2007?

How to add Chinese Pinyin (拼音) in Microsoft Word 2007? After searching google, I found a great video to add Chinese Pinyin (拼音) to Chinese characters in Word. In Word 2007 (and probably other newer versions), we can do this by using the function of ‘Phonetic Guide’. The procedure consists of two steps (as shown in the figure below): Step... Read more »
December 6, 2016

Install Jekyll on Windows

What is Jekyll? Jekyll is a set of ruby packages to make website and blog maintenance automatic. It can convert plain text files (particularly Markdown files) into static html files which then can be hosted by a web server. The most attractive feature is that Github.com uses Jekyll as the... Read more »
December 5, 2016

The history of sequencing in industry

Sequencing technologies have transformed biological research dramatically. They themselves also experienced fast evolution: cost reduction and bankruptcies. See the history published by Qiagen below. Next-Generation Sequencing Commercial Milestones Infographic from QIAGEN... Read more »
November 19, 2016

My paper on Drosophila X chromosome regulation is online now

I am pretty happy that my paper on the comparison of the mRNA translation rates between X chromosome and autosomes is online now at http://mbe.oxfordjournals.org/content/early/2015/10/19/molbev.msv227.abstract. This work shows that Drosophila X-linked genes have overall lower (~17% or more, depending on the examined samples) translation rates than autosomal genes, thus predicting a... Read more »
October 22, 2015

A note on Globus

Today I tried to download the data from the Phytozome database. One method is using Globus. It turned out that this method is very fast. Now I share a couple of notes on the concept of Globus. Data are transferred between endpoints using Globus webpage https://www.globus.org/ (after login, choosing Manage... Read more »
October 3, 2015