1. Codon Code Corporation
Laiqa Hashim
Roll no 1026
Bs(Hon)Botany (M)
Education University
Renala Campus
2. 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
3. Codon Code Corporation
CodonCode Corporation develops CodonCode
Aligner, a leading software program for DNA
sequence analysis.
4. 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
5.
6. 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.
7.
8. 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
9. 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
10. 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.
11.
12. 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).
