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Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. [2] [3] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4]
The SAM format consists of a header and an alignment section. [1] The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. [4] SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is ...
However, when the alignment of offset is already equal to that of align, the second modulo in (align - (offset mod align)) mod align will return zero, therefore the original value is left unchanged. Since the alignment is by definition a power of two, [ a ] the modulo operation can be reduced to a bitwise AND operation.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
The default OperandSize and AddressSize to use for each instruction is given by the D bit of the segment descriptor of the current code segment - D=0 makes both 16-bit, D=1 makes both 32-bit. Additionally, they can be overridden on a per-instruction basis with two new instruction prefixes that were introduced in the 80386:
Han Xin Code finder pattern. Finder Pattern [3]: 4.2.3 consists from four Position Detection Patterns located at the four corners of the barcode. The size of Position Detection Pattern is 7×7 modules and it is constructed from 5 elements: dark 7 × 7 modules, light 6 × 6 modules, dark 5 × 5 modules, light 4 × 4 modules, dark 3 × 3 modules respectively.
Compressed Reference-oriented Alignment Map (CRAM) is a compressed columnar file format for storing biological sequences aligned to a reference sequence, initially devised by Markus Hsi-Yang Fritz et al. [1] CRAM was designed to be an efficient reference-based alternative to the Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) file ...
The guide tree in the initial versions of Clustal was constructed via a UPGMA cluster analysis of the pairwise alignments, hence the name CLUSTAL. [11] cf. [12] The first four versions of Clustal were numbered using Arabic numerals (1 to 4), whereas the fifth version uses the Roman numeral V. [11] cf. [13] [5] The next two versions proceed alphabetically using the Latin alphabet, with W ...