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AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2330 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2283 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...Shouji: a fast and efficient pre-alignment filter for sequence alignment
By Jit 1875 days agogithub.com - The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration...Caretta – A multiple protein structure alignment and feature extraction suite
By Rahul Nayak 1466 days agowww.bioinformatics.nl - Caretta – a multiple protein structure alignment and feature extraction suite Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments...Seal: SEquence ALignment evaluation suite
By Jit 2546 days agocompbio.case.edu - Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including: Reading a pre-existing reference...Demo 4: Using BLAST/BLAT in Ensembl
By Radha Agarkar 4121 days agoWe demonstrate the BLAST/BLAT tool in Ensembl. Search for a sequence in Ensembl, and identify hits to the genome, or to genes, with this tool.Genome Workbench 2.10.7
By Gudiya Pal 3096 days agoGenome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.
Converting BLAST output into CSV
Last updated 2569 days ago by Poonam MahapatraSuppose we wanted to do something with all this BLAST output. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST, or something. As with most programs that run on UNIX, the text output is in some specific...BLAST+ 2.11.0 release is now available on FTP site !
By Jit 1499 days agoThe main advance is the ability to provide usage reports to NCBI to help us improve BLAST.Chemical Elements of Bioinformatics
By Rahul Agarwal 4128 days agoAmaze by new elements table by Eagle genomics !!!
