Curator Dashboard

Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together.

• Resource
• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software commands for Extra EMBOSS and protein domain alignment. The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for protein domain search. It is a part of Embassy software package.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for an efficient maximal exact match (MEM) computation program that does not use full text indexes, uses less space and is amenable to parallelization. It can be used as a stand alone application or a drop-in replacement for MUMmer3 system for rapidly aligning entire genomes.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

University in Durham, England.

• Organization
• SciCrunch
• 9 years ago - submitted by Isabella Froman

Research university in Dublin, Ireland, and a member institution of the National University of Ireland.

• Organization
• SciCrunch
• 9 years ago - submitted by Isabella Froman

University in Bratislava, Slovakia.

• Organization
• SciCrunch
• 9 years ago - submitted by Isabella Froman

Public university located in city of Tübingen, Baden-Württemberg, Germany known as centre for study of medicine, law, theology and religion. Alumni include numerous presidents, ministers, EU Commissioners and judges of the Federal Constitutional Court, eleven Nobel laureates, especially in fields of medicine and chemistry.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for handling multimedia files. FFmpeg can record, convert and stream audio and video.

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• RRID-Legacy
• 9 years ago - submitted by Samuel Nastase

Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html

• RRID-Legacy
• 9 years ago - submitted by Marin Manuel

Software toolkit for a cross-platform JSON-framework for describing command-line tools and their parameters. It is accompanied by a Python tool which facilitates the creation, validation, simulation, execution, publishing, evaluation, and testing of tools described in this format.

• nidash
• 9 years ago - submitted by Greg Kiar

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.

• Resource
• SciCrunch
• 9 years ago - submitted by Isabella Froman