Biotechnology andBioinformatics:BioinformaticsBiotechnology andBioinformatics:Bioinformatics
Essential Idea: Bioinformatics is the use ofcomputers to analyze sequence data inbiological research.Essential Idea: Bioinformatics is the use ofcomputers to analyze sequence data inbiological research.
TOKTOK
Knowledge claims justified by reference to databasesraise unique knowledge questions. How reliable areknowledge claims justified by reference to datasources developed for different purposes by differentresearchers using different methods?Knowledge claims justified by reference to databasesraise unique knowledge questions. How reliable areknowledge claims justified by reference to datasources developed for different purposes by differentresearchers using different methods?
DatabasesDatabases
A database is a set of related data that has beenorganized and made available for access by manyusers.A database is a set of related data that has beenorganized and made available for access by manyusers.
This data can be easily accessed by users anywherein the world.This data can be easily accessed by users anywherein the world.
Due to the rapid increase in data acquisition and theease of input of this data into such databases, theamount of information being stored is increasingexponentially--essentially doubling every 18 months.Due to the rapid increase in data acquisition and theease of input of this data into such databases, theamount of information being stored is increasingexponentially--essentially doubling every 18 months.
DatabasesDatabases
DatabasesDatabases
In the biological sciences, DNA sequence and proteinsequence data is the most often accessed.In the biological sciences, DNA sequence and proteinsequence data is the most often accessed.
These databases can be searched to compare newlyidentified sequences with sequences of knownfunction in other organisms.These databases can be searched to compare newlyidentified sequences with sequences of knownfunction in other organisms.
This allowsresearchers to usemultiple sequencealignment to look atthe evolutionaryrelationship of theorganisms beingstudied--such aswith phylogenetics.This allowsresearchers to usemultiple sequencealignment to look atthe evolutionaryrelationship of theorganisms beingstudied--such aswith phylogenetics.
DatabasesDatabases
Multiple SequenceAlignmentMultiple SequenceAlignment
When studyingevolutionaryrelationships,scientists oftenlook at thesequences ofmultipleorganisms.When studyingevolutionaryrelationships,scientists oftenlook at thesequences ofmultipleorganisms.
Multiple SequenceAlignmentMultiple SequenceAlignment
The gene function andthe gene sequence canbe studied in modelorganisms with similarsequences to learn moreabout them.The gene function andthe gene sequence canbe studied in modelorganisms with similarsequences to learn moreabout them.
This allows researchersto make inferences,develop hypotheses, andto design and testtreatment protocols forpeople with geneticdisorders.This allows researchersto make inferences,develop hypotheses, andto design and testtreatment protocols forpeople with geneticdisorders.
Sequence AlignmentSequence Alignment
Sequence alignment software is what allows peopleto make a comparison of sequences from differentorganisms.Sequence alignment software is what allows peopleto make a comparison of sequences from differentorganisms.
This software can be accessed online.This software can be accessed online.
For instance, the SDSC Biology Workbench we’ve used.For instance, the SDSC Biology Workbench we’ve used.
Searching databases for comparative purposesallows newly identified sequences to be comparedwith sequences of known function in other organisms.Searching databases for comparative purposesallows newly identified sequences to be comparedwith sequences of known function in other organisms.
BLASTBLAST
BLAST stands for Basic Local Alignment Search Tool.BLAST stands for Basic Local Alignment Search Tool.
It is an algorithm for comparing biological sequenceinformation.It is an algorithm for comparing biological sequenceinformation.
Users input and access data from anywhere.Users input and access data from anywhere.
There are many different ways in which this can beused.There are many different ways in which this can beused.
BLASTn is a nucleotide sequence alignment tool.BLASTn is a nucleotide sequence alignment tool.
BLASTp is a protein alignment tool.BLASTp is a protein alignment tool.
BLASTnBLASTn
Using this program, a DNA sequence can be inputand the software will return the most similar DNAsequences from the DNA database specified by theuser.Using this program, a DNA sequence can be inputand the software will return the most similar DNAsequences from the DNA database specified by theuser.
BLASTpBLASTp
As with the BLASTn, BLASTp allows the user toquery a protein sequence and get the most similarprotein sequence from the specified database.As with the BLASTn, BLASTp allows the user toquery a protein sequence and get the most similarprotein sequence from the specified database.
ESTEST
EST stands for Expressed Sequence Tag.EST stands for Expressed Sequence Tag.
Living organisms produce mRNAs from splicingtogether exons.Living organisms produce mRNAs from splicingtogether exons.
In vitro studies of tissuesamples of organismsabout which little isknown allows for thereverse transcription ofthese mRNA transcriptsto yield cDNA thatcorresponds to thegenes expressed in thattissue.In vitro studies of tissuesamples of organismsabout which little isknown allows for thereverse transcription ofthese mRNA transcriptsto yield cDNA thatcorresponds to thegenes expressed in thattissue.
ESTEST
Thus, an EST is a short “sub-sequence” of cDNA. Itis often used to identify gene transcripts, and plays animportant role in gene discovery and sequencedetermination.Thus, an EST is a short “sub-sequence” of cDNA. Itis often used to identify gene transcripts, and plays animportant role in gene discovery and sequencedetermination.
Simply put, the cDNA is complementary to mRNA andrepresents portions of expressed genes.Simply put, the cDNA is complementary to mRNA andrepresents portions of expressed genes.
This technique allows for a comparison ESTs fromlesser-known species with those from a specieswhose genome has been well-characterized enablingresearchers to identify the function of gene loci in thenew organism.This technique allows for a comparison ESTs fromlesser-known species with those from a specieswhose genome has been well-characterized enablingresearchers to identify the function of gene loci in thenew organism.
ESTEST
The development of a complete EST library is animportant step in the mapping of a new genome.The development of a complete EST library is animportant step in the mapping of a new genome.
ESTs can be mapped to specific chromosomelocations using a variety of methods (radiation hybridmapping, Happy mapping, FISH).ESTs can be mapped to specific chromosomelocations using a variety of methods (radiation hybridmapping, Happy mapping, FISH).
ESTEST
EST UsesEST Uses
ESTs give information that allows for the design ofDNA microarrays and subsequent determination ofgene expression.ESTs give information that allows for the design ofDNA microarrays and subsequent determination ofgene expression.
EST UsesEST Uses
The use of EST informationgives researchersknowledge about thefunction of a gene.The use of EST informationgives researchersknowledge about thefunction of a gene.
This information can beused in the diagnosis andtreatment of disease.This information can beused in the diagnosis andtreatment of disease.
Researchers are currentlydesigning methods to minedatabases for ESTinformation and genediscovery.Researchers are currentlydesigning methods to minedatabases for ESTinformation and genediscovery.
Gene Knockout TechnologyGene Knockout Technology
Gene knockout technology is also used to determinethe function of a gene.Gene knockout technology is also used to determinethe function of a gene.
This technique is commonly used on mice and othermodel organisms.This technique is commonly used on mice and othermodel organisms.
In this process, a gene that has been sequenced, butfor which little to no function is known is “knocked out”of the organism.In this process, a gene that has been sequenced, butfor which little to no function is known is “knocked out”of the organism.
Gene Knockout TechnologyGene Knockout Technology
Organisms in which the gene has been knocked outare compared to normal organisms enablingresearchers to draw conclusions about the function ofthe gene.Organisms in which the gene has been knocked outare compared to normal organisms enablingresearchers to draw conclusions about the function ofthe gene.
How it Works:How it Works:
The genetic information of individual cells is altered insome way creating a transgenic animal with analtered gene.The genetic information of individual cells is altered insome way creating a transgenic animal with analtered gene.
Once this has been accomplished, the goal is to getembryonic stem cells transformed and inserted intoearly embryos.Once this has been accomplished, the goal is to getembryonic stem cells transformed and inserted intoearly embryos.
This results in animals with a genetic change in theirgerm-line cells that can pass the genetic alteration onto their offspring.This results in animals with a genetic change in theirgerm-line cells that can pass the genetic alteration onto their offspring.
How it Works:How it Works:
