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The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome.
Pubmed ID: 36310248 RIS Download
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A database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).
View all literature mentionsA sequence analysis tool providing a simple but detailed analysis of human genes and their variations. For each gene, a gene-gene relationship network can be generated based on protein-protein interaction data, metabolic pathway connections and extended through phylogenetic relations. Snap provides tools for designing sequence primers and evaluating RNA splicing effects of single SNPs - known from the databases or defined by you. Primers can be designed for the amplification or sequencing of cDNA, genomic DNA, introns only or exons only.
View all literature mentionsCommercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.
View all literature mentionsSoftware to: view dicom files and assemble them into 3D volumes. View and convert between Analyze, Nifti, and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans.
View all literature mentionsSoftware for searching DNA sequence databases for RNA structure and sequence similarities.
View all literature mentionsIntegrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
View all literature mentionsSoftware Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.
View all literature mentionsWeb server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file).
View all literature mentionsSoftware tool to quantitatively measure genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.
View all literature mentionsA software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
View all literature mentionsA powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
View all literature mentionsOpen source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
View all literature mentionsSoftware tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
View all literature mentionsSoftware that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.
View all literature mentionsR software package for the detection of gross chromosomal abnormalities from gene expression microarray data.
View all literature mentionsPackage of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree.
View all literature mentionsPublic knowledge base for information on evolutionary timescale of life. Data from thousands of published studies are assembled into searchable tree of life scaled to time.
View all literature mentionsSoftware tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference.
View all literature mentionsSoftware that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis.
View all literature mentionsSoftware package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
View all literature mentionsSystem that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly.
View all literature mentionsSoftware R package for statistical analysis and visualization of functional profiles for genes and gene clusters.
View all literature mentionsCentral online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading.
View all literature mentionsThe Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome
View all literature mentionsWeb server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file).
View all literature mentionsSoftware tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format).
View all literature mentionsSoftware for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
View all literature mentionsGene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute.
View all literature mentionsSoftware package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark.
View all literature mentionsSoftware application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .
View all literature mentionsGraph-based alignment of next generation sequencing reads to a population of genomes.
View all literature mentionsSoftware tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software program can be used to generate SNP haplotype sequence data of unrelated individuals and nuclear families with a fixed or random number of children.
View all literature mentionsSoftware for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.
View all literature mentionsSoftware tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.
View all literature mentionsSoftware tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).
View all literature mentionsSoftware tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation.
View all literature mentionsSoftware tool for de novo detection of full length LTR retrotransposons in large sequence sets. Delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs.
View all literature mentionsOpen collection of Transposable Element DNA sequence alignments, hidden Markov Models, consensus sequences, and genome annotations.Dfam 3.2 provides early access to uncurated, de novo generated families.
View all literature mentionsDatabase of repetitive DNA elements.Database of prototypic sequences representing repetitive DNA from different eukaryotic species. Used in genome sequencing projects worldwide as reference collection for masking and annotation of repetitive DNA.
View all literature mentionsSoftware package for identification of long terminal repeat retrotransposons (LTR-RTs). Removes false positives from initial software predictions. Achieves very high specificity, accuracy, and precision without significantly sacrificing sensitivity, hence significantly outperforming existing methods. Can construct LTR libraries directly from self-corrected PacBio reads prior to genome assembly.
View all literature mentionsSoftware tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies.
View all literature mentionsWeb software capable of scanning large-scale sequences for full-length LTR retrotranspsons.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Tool to annotate core genes in eukaryotic genomes (that was replaced by BUSCO). Its resulting core gene dataset can be used to train a gene finder or to assess the completeness of the genome or annotations.
View all literature mentionsSoftware tool to purge haplotigs and overlaps in assembly based on read depth.Used for haplotypic duplication identification. Designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.
View all literature mentionsSoftware tool as haplotype resolved de novo assembler for PacBio Hifi reads. Can assemble human genome in several hours.Introduces new graph binning algorithm and achieves haplotype resolved assembly given trio data. Takes advantage of long high fidelity sequence reads to represent haplotype information in phased assembly graph. Preserves contiguity of all haplotypes.
View all literature mentionsSoftware tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data.
View all literature mentionsSystem unleashes groundbreaking innovations that leverage our proven technology. Now you can get scalable throughput and flexibility for virtually any sequencing method, genome, and scale of project.
View all literature mentionsSequencer by Pacific Biosciencies. System provides advantages of SMRT Sequencing and now makes it more affordable for all scientists to drive discovery with comprehensive views of genomes and transcriptomes. Generates 8 times more data than original Sequel System. Provides access to highly accurate long reads (HiFi reads). Reduces project time for faster results. Makes sequencing more affordable.Supports range of SMRT Sequencing applications.
View all literature mentionsSoftware for acquisition and analysis of flow cytometry data. FloMax data analysis works with data from flow cytometers that support the flow cytometry file standard (FCS). FloMax operates on computers with Windows 95, 98, and 2000.
View all literature mentionsOpen source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach.
View all literature mentionsSoftware utility for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. It scans the raw reads and produces a compact representation of all non-unique reads accompanied with number of their occurrences. The algorithm implemented makes use mostly of disk space rather than RAM, which allows to use KMC even on rather typical personal computers.
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