Machine for protein domain search

A customer involved in plant breeding research asked us about a machine for searching DNA base sequences by BLAST and protein domain searches by HMMER.
It is assumed to be used by a faculty member and multiple students, and to access the machine via a wired LAN on campus.
Also, the number of query sequences in BLAST is about several hundred to several thousand, and the number of database sequences is about 10. Domain search by HMMER assumes about 10 query sequences.
As for other applications, if the machine performance is sufficient, we would like to perform de novo genome analysis of plants.
Assumed machine specs are as follows.

・CPU: Intel Core i7 16 cores or more
・ Memory: 64GB
・Storage 1: SSD 1TB S-ATA
・Storage 2: HDD 8TB S-ATA
・Video card: About Geforce GT1030
・Network: Gigabit Ethernet compatible

We propose the following configuration.

CPU AMD Ryzen9 7950X (4.50Hz 16 cores)
memory 64GB
Storage 1 1TB SSD S-ATA
Storage 2 8TB HDD S-ATA
video NVIDIA Geforce GT1030
network on board (2.5G x1 10/100/1000Base-T x1) Wi-Fi x1
Housing + power supply Middle tower case + 850W
OS RockyLinux 8

The database is assumed to be stored on an 8TB HDD, but depending on the size, the storage capacity may be insufficient, so the customer has confirmed that there is no problem in terms of capacity.

It is a configuration that allows execution of de novo analysis, but if it is considered as a high-priority requirement, it would be better to install 128GB, which is the maximum memory capacity according to the specifications.

Also, if you only use it for network access and use it as a small-scale simple server in the laboratory, the configuration of this example will be a cost-oriented choice.However, if it is assumed that it will be used by undergraduate students, the specifications will obviously be insufficient.
Depending on the conditions such as the importance of the machine and the required availability, it is necessary to consider a more full-fledged server configuration, so we inform the customer along with the proposal.

The configuration of this case study is based on the conditions given by the customer.
Please feel free to contact us even if you are considering different conditions from what is posted.

■FAQ

・What is BLAST?
BLAST (Basic Local Alignment Search Tool) is a homology search program that performs sequence alignment of DNA base sequences and protein amino acid sequences.By searching a sequence database or library with a sequence at hand, a group of similar sequences with a score above a certain threshold can be found.

reference:BLAST (National Center for Biotechnology Information) *Jumps to an external site

 

・What is HMMER?
HMMER is free software for sequence analysis.Homologous protein or nucleotide sequences are identified and a sequence alignment performed.

reference:HMMER *Jumps to an external site

 

・What is de novo analysis?
A method for determining the amino acid sequence of peptides from tandem mass spectrometry.It does not require a reference sequence and is used for genetic analysis of non-model organisms.