A short introduction to protein structures modification and ModFinder
A lot of protein structures are determined on a large scale and submitted in Protein Data Bank (PDB) www.rcsb.org . After the experimental determination of these structures, they are used in many scientific studies and experiments are performed upon them such as mutagenesis, docking, and so on.
Sometimes, it is important to study protein sequence modifications such as glycosylation, acetylation, phosphorylation, and sulfonation. These modifications are a dynamic process in living cells leading to diverse protein functions. Protein modifications may occur before, after or during the protein synthesis. They are commonly referred to as post-translational modifications (PTMs) . The mapping of these modifications helps us understand protein functions under a specific condition such as health and diseases which are related to a specific pattern of gene expression. Protein modifications are submitted to and made available in UniProtKB database  on the basis of the data obtained from various sources such as literature, observation in 3D structures, related proteins, annotations in specific databases, and so on. There are several available databases which collect annotations and modifications in the proteins such as RESID , PSI-MOD ontology , and Unimod .
A new software has been developed by Gao et al., (2017)  to map the annotations in protein structures available in PDB. It is a BioJava  package, known as ModFinder developed to identify protein modifications in 3D structures (https://github.com/biojava/biojava/tree/master/biojavamodfinder). The ModFinder module is run weekly after the update of the PDB database and the updated modifications are loaded as annotations into the RCSB PDB database. They can be easily searched in RCSB PDB using “Advanced Search/Sequence Features” option on the website [9,10]. The protein modifications can be easily traced into the structure by using ModFinder .
ModFinder is a novel software which offers the identification and visualization of protein modifications in the protein 3D structures available in PDB. Since it may be proved beneficial for most of the researchers, therefore, it would be easy to map the annotations in DNA sequences also.
1. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne.
(2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.
2. Farriol‐Mathis, N., Garavelli, J. S., Boeckmann, B., Duvaud, S., Gasteiger, E., Gateau, A., … & Bairoch, A. (2004). Annotation of post‐translational modifications in the Swiss‐Prot knowledge base. Proteomics, 4(6), 1537-1550.
3. Apweiler, R., Bairoch, A., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., … & Martin, M. J. (2004). UniProt: the universal protein knowledgebase. Nucleic acids research, 32(suppl 1), D115-D119.
4. Garavelli, J.S. (2004) The RESID Database of protein modifications as a resource and annotation tool. Proteomics, 4, 1527-1533.
5. Montecchi-Palazzi, L. et al. (2008) The PSI-MOD community standard for representation of protein modification data. Nat. Biotechnol., 26, 864-866.
6. Creasy, D. M., & Cottrell, J. S. (2004). Unimod: Protein modifications for mass spectrometry. Proteomics, 4(6), 1534-1536.
7. Gao J., Prlić A., Bi C., Bluhm W. F., Dimitropoulos D., Xu D., Bourne P. E., Rose P. W. BioJava-ModFinder: Identification of Protein Modifications in 3-D Structures from the Protein Data Bank. Bioinformatics btx101. DOI: https://doi.org/10.1093/bioinformatics/btx101 Published: 17 February 2017
8. Prlić, A. et al. (2012) BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics, 28, 2693-2695.
9. Rose, P.W. et al. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
10. Rose, P.W., et al (2015) The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res. 43, D345-D356
HMMER- Uses & Applications
HMMER  is a well-known bioinformatics tool/software. It offers a web server and a command-line tool for users. Here are some additional applications of HMMER. (more…)
Easy installation of some alignment software on Ubuntu (Linux) 18.04 & 20.04
There are commonly used alignment programs such as muscle, blast, clustalx, and so on, that can be easily installed from the repository. In this article, we are going to install such software on Ubuntu 18.04 & 20.04. (more…)
FEGS- A New Feature Extraction Model for Protein Sequence Analysis
Protein sequence analyses include protein similarity, Protein function prediction, protein interactions, and so on. A new feature extraction model is developed for easy analysis of protein sequences. (more…)
Installing RDPTools on Ubuntu (Linux)
RDP provides analysis tools called RDPTools. These tools are used to high-throughput sequencing data including single-strand, and paired-end reads . In this article, we are going to install RDPTools on Ubuntu (Linux). (more…)
NGlyAlign- A New Tool to Align Highly Variable Regions in HIV Sequences
It is necessary to detect highly variable regions in envelopes of viruses as it allows the establishment of the viruses in the human body. A new tool is developed to build and align the highly variable regions in HIV sequences. (more…)
How to install ClustalW2 on Ubuntu?
Clustal packages [1,2] are quite useful in multiple sequence alignments. Especially, when you need specific outputs from the command-line. In this article, we will install CustalW2 command-line tool on Ubuntu. (more…)
Installing HMMER package on Ubuntu
HMMER tool is used for searching sequence homologs using profile hidden Markov Models (HMMs) . It is also one of the most widely used alignment tools. In this article, we will install the latest HMMER package on Ubuntu. (more…)
Installing FASTX-toolkit on Ubuntu
FASTX-toolkit is a command-line bioinformatics software package for the preprocessing of short reads FASTQ/A files . These files contain multiple short-read sequences obtained as an output of next-generation sequencing. In this article, we are going to install FASTX-toolkit on Ubuntu. (more…)
Aligning DNA reads against a local database using DIAMOND
DIAMOND is a program for high throughput pairwise alignment of DNA reads and protein sequences . It is used for the high-performance analysis of large sequence data. In this article, we will make a local database of protein sequences and align protein sequences against the reference database. (more…)
Installing MEME suite on Ubuntu
MEME suite is used to discover novel motifs in unaligned nucleotide and protein sequences [1,2]. In this article, we will learn how to install MEME on Ubuntu. (more…)
Installing BLAT- A Pairwise Alignment Tool on Ubuntu
BLAT is a pairwise sequence alignment algorithm that is used in the assembly and annotation of the human genome . In this article, we will install BLAT on Ubuntu. (more…)
Homology search against a local dataset using NCBI-BLAST+ command-line tool
NCBI-BLAST+  command-line tool offers multiple functions to be performed on a large dataset of sequences. Previously, we have shown how to blast against a local dataset of sequences. This article will explain the search of homologous sequences for a query sequence against a local database of sequences and how to obtain the top 100 hits out of the searched results. (more…)
How to use Clustal Omega and MUSCLE command-line tools for multiple sequence alignment?
Clustal Omega [1,2] and MUSCLE are bioinformatics tools that are used for multiple sequence alignment (MSA). In one of our previous articles, we explained the usage of the ClustalW2 command-line tool for MSA and phylogenetic tree construction. In this article, we will use Clustal Omega and MUSCLE for MSA exploring other arguments that facilitate different output formats. (more…)
Multiple Sequence Alignment and Phylogenetic Tree construction using ClustalW2 command-line tool
ClustalW2 is a bioinformatics tool for multiple sequence alignment of DNA or protein sequences. It can easily align sequences and generate a phylogenetic tree online (https://www.genome.jp/tools-bin/clustalw). However, in some cases, we need to perform these operations on a large number of FASTA sequences using the command-line tool of ClustalW2 . (more…)
Sequence search against a set of local sequences (local database) using phmmer
PHMMER is a sequence analysis tool used for protein sequences (http://hmmer.org; version 3.1 b2). It is available online as a web server and as well as a part of the HMMER stand-alone package (http://hmmer.org; version 3.1 b2). HMMER offers various useful features such as multiple sequence alignment including the file format conversion. (more…)
Biotite: A bioinformatics framework for sequence and structure data analysis
Sequence and structural data in bioinformatics are ever-increasing and the need for its analysis is ever-demanding likewise. As bioinformaticians analyze the data with their keen knowledge and reach important conclusions, similarly, bioinformaticists provide with the enhanced and advanced tools and software for data analysis. (more…)
Simulated sequence alignment software: An alternative to MSA benchmarks
In our previous article, we discussed different multiple sequence alignment (MSA) benchmarks to compare and assess the available MSA programs. However, since the last decade, several sequence simulation software have been introduced and are gaining more interest. In this article, we will be discussing various sequence simulating software being used as alternatives to MSA benchmarks. (more…)
Benchmark databases for multiple sequence alignment: An overview
Multiple sequence alignment (MSA) is a very crucial step in most of the molecular analyses and evolutionary studies. Many MSA programs have been developed so far based on different approaches which attempt to provide optimal alignment with high accuracy. Basic algorithms employed to develop MSA programs include progressive algorithm , iterative-based , and consistency-based algorithm . Some of the programs incorporate several other methods into the process of creating an optimal alignment such as M-COFFEE  and PCMA . (more…)
The basic local alignment search tool (BLAST) [1,2] is known for its speed and results, which is also a primary step in sequence analysis. The ever-increasing demand for processing huge amount of genomic data has led to the development of new scalable and highly efficient computational tools/algorithms. For example, MapReduce is the most widely accepted framework which supports design patterns representing general reusable solutions to some problems including biological assembly  and is highly efficient to handle large datasets running over hundreds to thousands of processing nodes . But the implementation frameworks of MapReduce (such as Hadoop) limits its capability to process smaller data. (more…)
Role of Information Theory, Chaos Theory, and Linear Algebra and Statistics in the development of alignment-free sequence analysis
Sequence alignment is customary to not only find similar regions among a pair of sequences but also to study the structural, functional and evolutionary relationship between organisms. Many tools have been discovered to achieve the goal of alignment of a pair of sequences, separately for nucleotide sequence and amino acid sequence, BLOSSUM & PAM  are a few to name. (more…)
You must be logged in to post a comment Login