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http://www.ch.embnet.org/software/COILS_form.html

COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.

Proper citation: COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.

Proper citation: Trim Galore (RRID:SCR_011847) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenGene/AfterQC

Software that performs automatic filtering, trimming, error removing, and quality control for fastq data.

Proper citation: AfterQC (RRID:SCR_016390) Copy   

•   Source: SciCrunch Registry

https://github.com/dvera/albacore

Data processing basecaller for the Oxford Nanopore sequencer that identifies DNA sequences directly from raw data. It enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data.

Proper citation: Albacore (RRID:SCR_015897) Copy   

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http://www.cbs.dtu.dk/services/SignalP/

Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.

Proper citation: SignalP (RRID:SCR_015644) Copy   

•   Source: SciCrunch Registry

http://dynamine.ibsquare.be/submission/

An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DynaMine (RRID:SCR_014559) Copy   

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https://github.com/isovic/racon

Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.

Proper citation: Racon (RRID:SCR_017642) Copy   

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https://github.com/TransDecoder/TransDecoder

Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.

Proper citation: TransDecoder (RRID:SCR_017647) Copy   

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https://www.sanger.ac.uk/science/tools/reapr

Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.

Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/ExonerateTransferAnnotation

Software tool as pipeline to make anntotations using cDNA and CDS sequences.

Proper citation: ExonerateTransferAnnotation (RRID:SCR_017557) Copy   

•   Source: SciCrunch Registry

http://cbcsrv.watson.ibm.com/phylopythia.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Data analysis service for accurate phylogenetic classification of variable-length DNA fragments.

Proper citation: PhyloPythia (RRID:SCR_000540) Copy   

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http://www.ncbi.nlm.nih.gov/dbSTS/

THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences.

Proper citation: dbSTS (RRID:SCR_000400) Copy   

•   Source: SciCrunch Registry

http://interolog.gersteinlab.org/

Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins.

Proper citation: Interolog/Regulog Database (RRID:SCR_000755) Copy   

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https://gtexportal.org/home/

Database and browser that provides a central resource to archive and display association between genetic variation and high-throughput molecular-level phenotypes. This effort originated with the NIH GTEx roadmap project: however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets.

Proper citation: GTEx eQTL Browser (RRID:SCR_001618) Copy   

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https://fungi.ensembl.org/Neurospora_crassa/Info/Index

It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available.

Proper citation: Neurospora crassa Database (RRID:SCR_001372) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/LSPD/

LSPD provides liver specific gene. It lists ~300 promoter regions responsible for liver specific transcriptions, collect ~400 experimentally verified regulatory regions and elements, provide information on transcription regulation of liver genes, compare transcription regulation of functionally or evolutionarily related genes, and retrieve sequences of the promoter region. Its regulatory elements provides information on transcription regulatory elements, reports the methods for verification of the elements, records binding affinity and regulatory function, and summarizes the site distribution and sequence consensus.

Proper citation: LSPD (RRID:SCR_002125) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/cdd

Database of annotations of functional units in proteins including multiple sequence alignment models for ancient domains and full-length proteins. This collection of models includes 3D structures that display the sequence/structure/function relationships in proteins. It also includes alignments of the domains to known three-dimensional protein structures in the MMDB database. The source databases are Pfam, Smart, and COG. Users can identify amino acids in protein sequences with the resources available as well as view single sequences embedded within multiple sequence alignments.

Proper citation: Conserved Domain Database (RRID:SCR_002077) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/swissprot/hpi/hpi.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP download, HTTP download or by using a mirroring program which automatically retrieves the file at regular intervals.

Proper citation: Human Proteomics Initiative (RRID:SCR_002373) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/ieb/research/acembly/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions.

Proper citation: AceView (RRID:SCR_002277) Copy   

•   Source: SciCrunch Registry