This document discusses patterns and profiles in bioinformatics. It provides an example of a conserved pattern ("L-X(6)-L-X(6)-L-X(6)-L") found in 'Leucine zipper motif' proteins. It then shows how a profile is created by adding occurrence numbers from a multiple sequence alignment. Profiles capture conserved residues and patterns better than single sequences. Conserved residues likely involve protein function. Patterns help classify homologs and identify other sequences. The document also introduces the bioinformatics database PROSITE for identifying protein domains and functional sites.
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Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
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The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
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Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
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http://sandymillin.wordpress.com/iateflwebinar2024
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Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
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1. H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi,
Karachi
Chem-727 (Bioinformatics)
Lecture-21
Patterns and Profiles in Bioinformatics
3. Conserved pattern in ‘Leucine zipper motif’ containing proteins
L-X(6)-L-X(6)-L-X(6)-L
4. EFGHIVW
EYAHMIW
DYAHSLW
EFGHPLW
[ED]- [FY]- H-[GA]- X- [VIL]- W
A pattern obtained from
multiple alignment of a
family of proteins.
But – there are slightly
more glutamates than
aspartates in the
alignment!
5. Making profile
let’s add some numbers to the
problem!
EFGHIVW
EYAHMIW
DYAHSLW
EFGHPLW
E
D
F
Y
H
G
A
I
M
S
P
L
V
W
One
15
5
0
0
0
0
0
0
0
0
0
0
0
0
Two
0
0
10
10
0
0
0
0
0
0
0
0
0
0
Three
0
0
0
0
0
10
10
0
0
0
0
0
0
0
Four
0
0
0
0
20
0
0
0
0
0
0
0
0
0
Five
0
0
0
0
0
0
0
5
5
5
5
0
0
0
Six
0
0
0
0
0
0
0
5
0
0
0
10
5
0
Seven
0
0
0
0
0
0
0
0
0
0
0
0
0
20
Positions
6. Significance of Patterns and Profiles
• Profiles express the patterns inherent in multiple alignment of a set
of homologous sequences.
• They permit greater accuracy in alignments of distantly-related
sequences.
• Highly conserved residues are likely to be part of the active site
• Conservation patterns facilitate identification of other homologous
sequences.
• Patterns help in classifying subfamilies within a set of homologues.
• Residues with little conservation and are subject to indels, are likely
to be in the surface loops of protein structures.
• Reliability of protein-structure prediction methods (in particular
homology modeling) increase due to information obtained from
multiple alignments
7. PROSITE; premier bioinformatics service for
identification of patterns and profiles
• PROSITE is a database of protein families and domains.It
consists of entries describing the domains, families and
functional sites as well as amino acid patterns, signatures, and
profiles in them.
• Applications include (a) identifying possible functions of
newly discovered proteins and (b) analysis of known proteins
for previously undetermined activity.
• Prosite outputs contain information about biologically
meaningful residues, like active sites, substrate- or co-factor-
binding sites, posttranslational modification sites or disulfide
bonds, to help function determination.
• E.g. prediction of phosphorylation/glycosylation sites in
protein sequences.
![EFGHIVW
EYAHMIW
DYAHSLW
EFGHPLW
[ED]- [FY]- H-[GA]- X- [VIL]- W
A pattern obtained from
multiple alignment of a
family of proteins.](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)