Software Dockey
Dockey is a robust and highly usable graphic user interface tool covering the whole streamlined pipeline of molecular docking that involves molecular sanitization, molecular preparation, docking execution, interaction detection and conformation visualization. In addition, Dockey is very competent to automatically dock thousands of ligands to multiple receptors in parallel accompanying with detection of various kinds of interactions. Due to its cross-platform compatibility, the generated project file can be shared between any systems and computers with the installation of Dockey.
Software Pyfastx
Pyfastx is a robust and versatile tool with high time- and memory-efficient random access to sequences from both plain and gzipped FASTA/Q files containing large sequence records. Pyfastx is also a fast parser for sequential iterating over sequence records from FASTA/Q files.We developed pyfastx as a user-friendly Python package due to the increasing popularity of Python as an ideal language for developing bioinformatics applications. Additionally, pyfastx is designed to have excellent compatibility and allows parsing of non-standard FASTA files with different line lengths in an individual sequence. Pyfastx also supplies command-line tools for users to extract subsequences, split FASTA/Q files and randomly sample sequences.
Database PSMD
PSMD comprises 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms, which covered almost all species with available genomic data. In addition to interactive browse interface, PSMD also offers a flexible filter function for users to quickly gain desired microsatellites from large data sets. PSMD allows users to export GFF3 formatted file and CSV formatted statistical file for downstream analysis. We also implemented an online tool for analysing occurrence of microsatellites with user‐defined parameters. Furthermore, Primer3 was embedded to help users to design high‐quality primers with customizable settings.
Database MACSNVdb
MACSNVdb is an open-access SNV database comprising ~74.51 million high-quality non-redundant SNVs called from 20 macaques that may assist researchers to investigate interspecies genetic divergence between macaques. MACSNVdb allows users to browse and retrieve individual, sepcific and non-redundant SNVs. In particular, users can retrieve non-synonymous SNVs that may have deleterious effects on protein structure or function within macaque orthologs of human disease and drug-target genes. MACSNVdb also integrates gene functional annotation information including GO term, KEGG pathway, Pfam and InterPro domains.
Software Krait
Krait is a robust and flexible tool for fast investigation of microsatellites in DNA sequences. Krait is designed to identify all types of perfect or imperfect microsatellites on a whole genomic sequence, and is also applicable to identification of compound microsatellites. Primer3 was seamlessly integrated into Krait so that users can design primer for microsatellite amplification in an efficient way. Additionally, Krait can export microsatellite results in FASTA or GFF3 format for further analysis and generate statistical report as well as plotting.