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BLAST / Basic Local Alignment Search Tool
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Allows to align query sequences against those present in a selected target database. BLAST is a suite of programs, provided by NCBI, which can be used to quickly search a sequence database for matches to a query sequence. The software provides an access point for these tools to perform sequence alignment on the web. The set of BLAST command-line applications is organized in a way that groups together similar types of searches in one application.
BLASTX / Translated BLAST: blastx
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Searches protein database using a translated nucleotide query. BLASTX is a BLAST search application that compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. This application can also work in Blast2Sequences mode and can send BLAST searches over the network to public NCBI server if desired.
CodingQuarry
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A highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts. RNA-seq data informs annotations both during gene-model training and in prediction. This approach capitalises on the high quality of fungal transcript assemblies by incorporating predictions made directly from transcript sequences. Correct predictions are made despite transcript assembly problems, including those caused by overlap between the transcripts of adjacent gene loci.
BRAKER
A pipeline for unsupervised RNA-seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS. As input, BRAKER1 requires a genome assembly file and a file in bam-format with spliced alignments of RNA-seq reads to the genome. First, GeneMark-ET performs iterative training and generates initial gene structures. Second, AUGUSTUS uses predicted genes for training and then integrates RNA-seq read information into final gene predictions. In our experiments, we observed that BRAKER1 was more accurate than MAKER2 when it is using RNA-seq as sole source for training and prediction. BRAKER1 does not require pre-trained parameters or a separate expert-prepared training step.
PEP_scaffolder
An efficient and fast genome scaffolding method, using proteins to scaffold genomes. The pipeline aims to recover protein-coding gene structures. We tested the method on human contigs; using human UniProt proteins as guides, the improvement on N50 size was 17% increase with an accuracy of ∼97%. PEP_scaffolder improved the proportion of fully covered proteins among all proteins, which was close to the proportion in the finished genome. The method provided a high accuracy of 91% using orthologs of distant species. Tested on simulated fly contigs, PEP_scaffolder outperformed other scaffolders, with the shortest running time and the highest accuracy.
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