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In 2010 [2] the soybean genome sequence was released along with gene models and many other types of genome annotations that were integrated in to SoyBase. SoyBase genetic linkage maps were integral to the assembly of the soybean genome. In 2018 the database received approximately 63,000 page requests from 2,600 users per month from 130 countries.
Tools for querying and downloading gene expression profiles are provided. Human Protein Atlas (HPA [10]): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors. Legume Information System (LIS): genomic database for the legume family [11]
Karyotype visualisation in Ensembl Genomes. The key feature of Ensembl Genomes is its graphical interface, which allows users to scroll through a genome and observe the relative location of features such as conceptual annotation (e.g. genes, SNP loci), sequence patterns (e.g. repeats) and experimental data (e.g. sequences and external sequence features mapped onto the genome). [1]
The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes [8] [9] EuGene: Integrative gene finding: Prokaryotes, Eukaryotes [10] [11] FGENESH: HMM-based gene structure prediction: multiple genes, both chains: Eukaryotes [12] FrameD: Find genes and frameshift in G+C rich prokaryote ...
TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S.cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members. TreeFam is also an ortholog database.
GenMAPP (Gene Map Annotator and Pathway Profiler) is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in the context of pathways (metabolic, signaling), connecting gene-level datasets to biological processes and disease. [1]