EMBOSS

GUI: a sequence analysis server

Introduction
There are many bioinformatics tools available during past two decades. Many free
tools are available for installation and use. However there have also been certain
shortfalls in installing and configuring some tools for several reasons. A few to
mention would be the compiling libraries for software, system speed to run the
programs and space consumption by the databases especially with bioinformatics
searches. To overcome such limitations, some bioinfomatics tools are made available
online. EMBOSS (European Molecular Biology Open Software Suite) is one among
the free open source bioinformatics software available for sequence analysis. The
GUI (Graphic user interface) of EMBOSS is one such software suite.

Availability and implementation
EMBOSS is available for download for Windows, Mac and unix systems
(http://emboss.sourceforge.net/download/). The GUI of EMBOSS is available online
(http://imed.med.ucm.es/EMBOSS/).

Figure 1 :EMBOSS GUI webpage


















About EMBOSS
EMBOSS provides programs for sequence analysis of proteins and nucleic acid.
Within EMBOSS there are around hundreds of programs including Sequence
alignment, database searching, protein motif and domain analysis, codon usage,
nucleotide pattern etc. All programs can be listed alphabetically or grouped by the
type of analysis.
This instruction note will provide guidelines for using EMBOSS GUI.

Analysis with Example: Human insulin
In this instruction, analysis of human protein insulin will be done using EMBOSSGUI
protein composition tool kit.

STEPS:
1. First and foremost it is mandatory to choose a protein on which analysis have
be carried out. For example human insulin.
2. Next would be to find the sequence ID or information for human insulin from
the protein database namely Uniprot (http://www.uniprot.org/uniprot/)
3. Fetch the sequence in a specific format (FASTA)


Sequence ID: P01308 (from Uniprot)
FASTA format:
>sp|P01308|INS_HUMAN Insulin OS=Homo sapiens GN=INS PE=1 SV=1
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED
LQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN

Program: PEPSTATS

4. Choose program from EMBOSS-GUI and Upload information on protein either
sequence ID or FASAT sequence

Figure 2: Pepstats program EMBOSS GUI webpage













Enter ID

here


Paste
sequence here







5. Each program from EMBOSS-GUI will show information about the program.
As seen in the above picture, the program pepstats gives statistics on the
protein amino acid information
6. The protein sequence ID should be provided, here P01308 in the respective
filed and then run pepstats
7. The following output file will be generated with information on protein
molecular weight, isoelectric point etc. The result can also be saved by right
click on the link.


Figure 3: Result of pepstats program






















Reference
EMBOSS: The European Molecular Biology Open Software Suite (2000)
Rice,P. Longden,I. and Bleasby,A.
Trends in Genetics 16, (6) pp276--277