Alignment of reads

A multiple sequence alignment of reads is constructed for each contig. The construction is performed by repeatedly aligning the next read with the current alignment. The reads are considered in increasing order of their positions in the contig. 

A portion of a multiple alignment of reads and a consensus sequence produced by CAP3 on the example data set. 

Measurements taken with this device are based on a point of reference at the zero position, which is defined as the alignment fixture at the top of the shaft - referred to as the 12 o clock position. In order to perform the alignment procedure, readings also are required at the 3, 6, and 9 o clock positions. 

A very small pressure difference is obtained for low rates of flow of gases, and the lower limit of velocity that can be measured is usually set by the minimum difference in pressure that can be measured. This limitation is serious, and various methods have been adopted for increasing the reading of the instrument although they involve the need for calibration. Correct alignment of the instrument with respect to the direction of flow is important this is attained when the differential reading is a maximum. 

BWA http //bio-bwa.sourceforge.net/ Alignment of sequence reads to a reference genome... 

UCSC genome browser http //genome.ucsc.edu/cgi-bin/ hgGateway Visualization of aligned sequence reads in the genome of interest... 

Figure 1 Positions of cloned cDNA sequences relative to the mouse delta opioid receptor open reading frame. The figure shows an alignment of the insert sequences for the four cDNA clones obtained from human brain cDNA libraries. Together the 44-11 and 78-4 cDNA inserts cover the entire open reading frame and include 3 and 5 flanking sequences.

Fig. 3. Alignment of N-terminal sequences of Alt a 1. N-terminal peptide sequences of Alt a 1 [48, 50, 51 ] were compared with the complete open reading frame of Alt a 1 [16, 18]. Identical amino acids are marked in grey. The numbering of the amino acids is according to the complete open reading frame. Curran et al. [48] as well as Aden [50] identified 2 different variants with minor differences in the respective N-terminal sequences. Dashes represent gaps in the sequence. Dots indicate that this part of the protein was not sequenced. The first 5 sequences were determined hy solid-phase Edman degradation of nAlt a 1. The last two sequences are deduced from cDNA sequences.

Figure 3.89. Normalized TP fluorescence intensity of polymer dispersed liquid crystals as a function of the polarization angle of the reading beam, which is defined as the angle between the writing and reading polarization states. Inset top Schematic alignment of liquid crystal directors in exposed (dots) and unexposed regions. Inset bottom Two fluorescing data bits obtained by irradiation at a polarization angle of 90°. (From Ref. [248] with permission of the American Institute of Physics.)...

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