Codon Code Corporation

Laiqa Hashim Roll no 1026 Bs(Hon)Botany (M) Education University Renala Campus

Content:

•Introduction•Sequence assembly with codon code alinger•Importance•Specific feature in codon code aligner•What new in codon code aligner 5•Speed and memory improvement•Reference

Codon Code Corporation CodonCode Corporation develops CodonCode Aligner, a leading software program for DNA sequence analysis.

Introduction: • CodonCode Corporation provides user frendly,affordabl and powerful software for DNA sequence assembly and alignment. • Our software helps to minimize the time needed to analyze DNA sequencing data through better algorithms and intuitive tools.• . CodonCode Corporation's development provides poweful and unique analysis methods for evolution research biogeography, mutation detection, and other biochemical area

Sequence Assembly with CodonCode Aligner:

CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection. Features include:• Multiple sequence assembly and sequence alignment algorithms.• Manual and automated sequence editing.• Align contigs to each other and get back to the underlying trace data with a simple double-click.• Reference sequences and difference tables.• Sensitive mutation detection.• Advanced methods for heterozygous indel analysis.

Importance:

With codon code you can:• Import sequences from text files• End clip• Assemble contigs• Align contigs to each other while keeping the links to the traces. • Find heterozygous mutations • Define regions of interest ("features"), for example low quality consensus region. • Generate phylogenetic trees and restriction maps • Export sequences and features

Specific Features in CodonCode Aligner:

• Assembling in groups (by name) • Comparing contigs • Import only matching sequences• Using reference sequences to bridge gaps and set sample orientation • Automatic reference sequence shortening• Starting BLAST searches • Restriction mapping • Tips for using CodonCode Aligner

What's new in CodonCode Aligner 5:

•CodonCode Aligner version 5 can create Bowtie 2 alignments and display paired end reads. Additional new features include moving multiple gaps with drag & drop, alignments with Clustal Omega, contig overview printing, and multiple speed and memory improvements for large projects and alignments.CodonCode Aligner version 5.0.2 fixes several bugs, and adds improved amino acid translation for codons with ambiguities.

Speed and Memory Improvements:

•CodonCode Aligner version 5 includes many optimizations for big projects and large assemblies and alignments. Results are a reduction in needed memory and Aligner being noticeable faster.•CodonCode Aligner 5.0.1 is compatible with Windows 8 and OS X Mavericks (10.9).

Content:

•www.codon code .com•www.codon code.com/aligne•codon code.org/•www.codon code.com/about.htm