Results for "structural and sequence variation"
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BIMA V3: an aligner customized for mate pair library sequencing
Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortu...reference genome is a challenging and time consuming process for mo...ad contamination, chimeras, etc.), and presence of structura...2709 days ago
MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs
MeGAMerge MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic...l based wrapper/tool that can accept any number of sequence (FASTA) files containing asse...ou will need to have the following tools installed and in $P...2704 days ago
- LAST can: Handle big sequence data, e.g: Compare two v...bsp;of each aligned column. Use sequence quality data properly....h frameshifts. Compare PSSMs to sequences Calculate the likelihood of chance similarities between random sequences. Do split and splic...
2704 days ago
- ...aligned nucleotide or protein sequences, and to perform a wide variety of...if-based analysis of DNA, RNA and protein sequences. It provides motif discovery...ifs with arbitrary insertions and deletions (GLAM2). In addition to...e provides tools for scanning sequences for matches to motifs (FIMO,...
2700 days ago
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
Prodigal (Prokaryotic Dynamic Programming Genefinding...Oak Ridge National Laboratory and the University of Tennessee....gene identification programs, and usually falls under 5%. GC-Conten...metagenomic mode and analyze sequences even when the organism is un...2695 days ago
GenomeRing: alignment visualization based on SuperGenome coordinates
The number of completely sequenced genomes is continuously rising, all...mparative analyses of genomic variation. Such analyses are ofte...that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supple...2674 days ago
- PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler...e positions where the forward and reverse primers match best above t...d and discard the ends of the sequence, including the primer.2.Pick...erver.uwaterloo.ca/~apmasell/pandaseq_m...
2669 days ago
FSA: Fast Statistical Alignment
...This is made possible by the sequence annealing technique for const...ding Methods for Optimization and Control of Multiple Alignments."...roblems such as aligning thousands of sequences or megabase-long sequences....of multiple alignment. This randomized inference can be over ten ti...2656 days ago
- The hive plot is a rational visualization method for dra...ng networks. Nodes are mapped to and positioned on radially distri...this mapping is based on network structural properties. Edges are drawn as curved links. Simple and inte...h; a method that is both general and tunab...
2645 days ago
- ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on s...bled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly con...olecule taking overlaping contigs and gaps...
2645 days ago
