The document discusses two bioinformatics software tools: DNA Baser and Darwin. DNA Baser is a tool for manual and automatic DNA sequence assembly, analysis, editing, and more. It allows for automation of sequence assembly through functions like end trimming, vector removal, and batch assembly of thousands of sequences. Darwin is an interpreted computer language for research in bioscience that provides libraries and functions for tasks like sequence comparison, alignment, phylogenetics, and more.

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

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

3. DNA BASER
What is dna baser ?
o 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...)

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