A new assembler called SAUTE is developed for sequence assembly that is based on target enrichment .
SAUTE stands for sequence assembly for target enrichment. It efficiently assembles repeat regions and reports multiple well-supported variants. Users can provide target sequences for assembly assistance. The authors have developed two assemblers namely, SAUTE and SAUTE_PROT.
How SAUTE works?
At first, SAUTE reads input files in fast or fastq or SRA format and trim reads. After that, it builds two De Bruijn Graphs followed by finding and assembling subgraphs. These subgraphs are further filtered using the alignment of reads and read pairs to the assembled graph. Further, it assembles additional sequences beyond the ends if a user opts to do so. Finally, it reports output in the format of graphical fragment assembly along with two fasta files.
As compared to TRINITY, RNASPADES, SPALIGNER, and SPADES in the case of RNA-seq, SAUTE_PROT outputs more coding sequences translating to benchmark proteins.
SAUTE is currently available for Linux only. It is available to download on GitHub.
For more information, read here.
- Souvorov, A., Agarwala, R. (2021). SAUTE: sequence assembly using target enrichment. BMC Bioinformatics 22, 375.
Video Tutorial: Calculating binding pocket volume using PyVol plugin.
How to generate topology from SMILES for MD Simulation?
[Tutorial] Installing jdock on Ubuntu (Linux).
jdock is an extended version of idock . It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).
How to upgrade cmake on Ubuntu (Linux)?
In bioinformatics, cmake is used to install multiple software including GROMACS, jdock, and so on. Here is a short tutorial on how to upgrade cmake on Ubuntu and get rid of the previous version. (more…)
How to install GMXPBSA on Ubuntu (Linux)?
[Tutorial] Installing Pyrx on Windows.
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS  with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.
Installing Autodock4 on MacOS.
How to install Autodock4 on Ubuntu?
DS Visualizer: Uses & Applications
Protein structure & folding information exploited from remote homologs.
Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)
Pathonoia- A new tool to detect pathogens in RNA-seq data.
Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia .
AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool . Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,. (more…)
How to calculate binding pocket volume using PyVol plugin in PyMol?
How to generate electron density map using Pymol?
Installing PyVOL plugin in Pymol on Ubuntu (Linux).
How to execute matlab from terminal in Ubuntu (Linux)?
How to install Kpax on Ubuntu (Linux)?
Kpax is a bioinformatics program to search and align protein structures . It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)
How to run do_dssp command (mkdssp) in Gromacs 2022?
In the latest version of GROMACS (2022) , there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)