Dna baser

dna baser and darwin

1. DNA BASER AND DARWIN SOFTWARE OF BIOINFORMATICS Khadija sehar Roll no# 3030 Bs( hons )Botany 3 rd semester (E) University of Education Okara compous

2. CONTENTS DNA BASER History Discription Automation Fuctions Diagram DARWIN History Compositin Libraries Kernel Functions References

3. DNA BASER What is dna baser ?   Tool for manual and automatic sequence assembly , analysis, editing , sample processing , metadata integration , file format conversion and mutation detection .

4. History DNA Baser was first released in 2004. Since then it was constantly updated. The list of features is based on 'user request' which means that the end user can ask for new features and vote in a poll which features to be implemented first. DNA Baser was the first program to offer automatic end trimming, automatic vector removal and automatic sequence assembly (batch assembly ).

5. Description DNA Baser Assembler is unique bioinformatics software for manual and automatic DNA sequence assembly, DNA sequence analysis, automatic sample processing, contig editing, metadata integration, file format conversion and mutation detection

6. Automation The proprietary assembly algorithm is optimized for accuracy and not for speed. This is needed in order to allow DNA Baser to automate the sequence assembly process. The program automatically removed the low quality ends, assemble the input samples, generates the contig /consensus then it automatically corrects the ambiguities. The data for ambiguity correction is obtain from the quality value assigned to each base in the input file. At the end the user-defined vectors are automatically removed from the contig and the metadata is added to the file. The contig is also automatically saved to disk as FASTA. The automation makes user's input unnecessary. This allows DNA Baser to take the sequence assembly to the next level through a sophisticated batch assembly module in which thousands of contigs can be obtained in minutes instead of days. The user defines the folder where the input files are and a pattern. Based on this pattern, the program automatically detects sequences belonging to the same set/ contig and assembles them together. The process described above is applied to each set. The contig is automatically saved to disk then the program moves to the next set with a speed of about one contig per second. The results of the process are written in a detailed log. The program highlights the assemblies that requires user input in red.

7. Functions DNA Baser concentrates on automation of sequence assembly process . With DNA Baser Sequence Assembler, you can : Assemble multiple DNA samples or align to a reference sequence Batch assemble or align in groups of sequences by name Automatically clip sample ends (low quality region trimming) Automatically detect and trim recognition (vector/primer) sequences Import and analyze sequences from ABI, SCF, FASTA and SEQ Preview chromatograms with a single click View and edit sequence traces Mark specific regions (like discrepancies, low-quality areas in chromatograms) with visible colors and quickly navigate to these regions Convert between different file formats (ABI, SCF, FASTA, multi-FASTA, GBK ...) Preview FASTA sequences and chromatograms as you navigate through your folders Easily overview your project using the synchronized chromatogram/assembly grid/ contig map

8. Diagram

9. DARWIN What is Darwin ? Darwin is an easy to use interpreted computer language especially tailored to research in bioscience. Purpose Its purpose is to serve as a biochemist’workbench where researchers can explore molecular sequence data quickly and easily .

10. History The darwin project began in 1991 and reflects much of the research done in the CBRG (computational biochemistry research group) at the ETH-Zurich. Composition It consist of two parts (1) Libraries (2) Libraries The libraries corresponds closely to what one expects from a software package: apre -defined set of functions offeresd by the system.The libraries reflect current and past trends in our research efforts but also incorporate many algorithms from litrature,particularly those related to sequnce comparison,phylogenetic tree construction,multiple sequence alignment and secondary structure prediction.

11. Kernel The kernel of the darwin is responsible for the lower level operations in the systems: executing commands and libraries,memory management,input / output,communication with operating system,load balancing etc.

12. Functions Helful in Basic mathematical operations Use in Pairwise alignment Dataset Conversions Peptide transition matrices Protein identification via peptide mass Phylogenetic tree and multiple sequence alignment construction Statistics and visualization .

13. References http://seqanswers.com/wiki/DNA_Baser Bioinformatics’ Darwin v.2.0:an interpreted computer language for the bioscience’G.H.,M.T,C and bernardin ..vol.16 no.22000 pages 101-103 http:// DNA baser .com