Abhimanyu Singh
A bioinformatics beginner
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Finding Patterns in Biological Sequences
By Jit 3515 days agoengr.case.edu - In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological verification of such patterns. Finally we list publicly...FSA: Fast Statistical Alignment
By Jit 3470 days agofsa.sourceforge.net - FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a...Laj: viewing and manipulating the output from pairwise alignment programs
By Abhimanyu Singh 3447 days agowww.bx.psu.edu - Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and...PANDASEQ
By Shruti Paniwala 3484 days agoneufeldserver.uwaterloo.ca - PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler reads two files in FASTQ format with quality information. If amplification primers were used (e.g., to isolate a variable...A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
By Abhimanyu Singh 3375 days agowww.sanger.ac.uk - PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference. IMAGE, an...Pacbio Long Reads Compatible Software and Tools
By Archana Malhotra 3432 days agogithub.com - The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual...Fastq format
By Jit 3384 days agoen.wikipedia.org - FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a...DIYA: a bacterial annotation pipeline for any genomics lab
By Jit 3326 days agosourceforge.net - DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and...Sr.Bioinformatics Analyst (NGS) at Ocimum
JOB FUNCTIONBio Tech/R&D/Scientist INDUSTRYBiotechnology/Pharmaceutical/Medicine SPECIALIZATIONBasic Research,Bio-Statistician,Clinical Research QUALIFICATION Any Post Graduate BA (Arts), B.Com. (Commerce), BE/ B.Tech (Engineering),...NGS course Medical Genomics, scheduled for 17-20 September 2013 in UZ Leuven (Belgium).
By Poonam Mahapatra 4743 days agoThe 4-day course is organized as a series of morning lectures and afternoon hands-on workshops.
