An Introduction

1. Molecular Biology Software links

2. BS-Botany 3rd(M)
 Name: Mudassar Iqbal
 Subject: Introduction to Computer
 Roll No: 1047
 University of Education Okara Campus

3. Introduction
 The identification of genetically homogeneous groups of individuals is a long
standing issue in population genetics. A recent Bayesian algorithm
implemented in the software structure allows the identification of such groups.
However, the ability of this algorithm to detect the true number of clusters (K)
in a sample of individuals when patterns of dispersal among populations are
not homogeneous has not been tested. The goal of this study is to carry out
such tests, using various dispersal scenarios from data generated with an
individual-based model. We found that in most cases the estimated ‘log
probability of data’ does not provide a correct estimation of the number of
clusters, K. However, using an ad hoc statistic ΔK based on the rate of change
in the log probability of data between successive K values, we found that
structure accurately detects the uppermost hierarchical level of structure for
the scenarios we tested. As might be expected, the results are sensitive to the
type of genetic marker used (AFLP vs. microsatellite), the number of loci
scored, the number of populations sampled, and the number of individuals
typed in each sample.

4. Related Data
 DAMBE (data analysis in molecular biology and
evolution) is an integrated software package for
converting, manipulating, statistically and graphically
describing, and analyzing molecular sequence data
with a user-friendly Windows 95/98/2000/NT
interface. DAMBE is free and can be downloaded from
http://web.hku.hk/~xxia/software/software.htm. The
current version is 4.0.36.

5. Links of Molecular Biology
Software
 1. Serial Cloner
Serial Cloner is fantastic all-in-one workbench; import and manipulate
sequences, construct plasmid and restriction site maps, determine
%GC and fragment TM, extract and ligate fragments, perform virtual
PCR… and lots more, all in one window using a very intuitive graphical
interface.
 2. Artemis
Artemis is a very user friendly DNA sequence viewer and annotation
tool released by the Sanger center. It is the main tool used by the guys
at the Sanger Centre for sequence annotation… and they do A LOT of
sequence annotation
 3. Molecular Weight Calculator
This free molecular weight calculator from the NCRR allows easy
calculation of molecular weights from formulae and amino acid
sequences, and does some other pretty useful stuff too.

6. 4. SeqVerter
A convenient sequence format converter application that can be used for… you've
guessed it… converting sequences between formats. A free part of the
commercial Gene Studio package.
5. Geneious
Geneious is a software package of genome & proteome research tools for protein,
DNA or molecular visualization, literature searching and storage…and more. The
Pro version does LOTS more.
6. Foxit Reader
Foxit Reader is a PDF viewer, reader and annotator. In terms of file size it is an
amazing 10 times smaller than Adobe Acrobat (2 MB compared to Acrobat's
20M), but it is packed with many more features. I especially love the annotation
capability that allows you to add typed notes, highlight text or add graphics. Use
it, save paper and save the rainforests!

7. 7. Fast PCR
Fast PCR is a really nice piece of software for primer design and in silico PCR.
Free for academic and non-commercial use only.
8. ApE
ApE is an all-in-one plasmid and sequence workbench. Sequences can be
uploaded to ApE manually, direct from the NCBI database or from ABI
chromatogram traces. ApE can be used for sequence annotation, restriction
mapping, primer design and sequence alignment. A great all round tool.
9. Cn3D
Cn3D… say it out loud… "see in 3D". This great piece of software from NCBI is a
sequence viewer with a difference. Not only does it perform 2D alignments, it
also allows the user to see the position residues in the 3D protein sequence.
Great for mutagenesis studies.
10. BioToolKit
This is one packed toolkit! Primer design, antibody design, microarray analysis,
calculators for molecular weight, molar concentration and OD, centrifguation
speed converter, label printing templates… and much more! Phew!

8. Conclusion
 The ability to analyze information about nucleic acids from a
variety of biological and chemical perspectives. You learn from
course and laboratory experiences how to apply biological and
chemical models, how to develop your own hypothesis, how to
evaluate conclusions based on evidence, and how to relate your
conclusions to biological and chemical properties of DNA.
 Reference:
 1>online.library.wiley.com
 2>www.ncbi.nlm.nih.gov
 3>bitesizebio.com