Some bioinformatics project ideas
Tumor Genome Visualization Tool
Tumor cells frequently have abnormal genomes. Gain and loss of whole chromosomes, duplications, deletions, translocations, inversions, and other chromosomal aberrations are common. Recent advances in sequencing technology allow us to obtain high-resolution, genome-wide information about these changes. However, the interpretation of this data requires the development of visualization tools. This project will develop such tools and use these tools to test various hypotheses about tumor genome architecture.
Required: Experience with graphics programming, preferably in a language that interfaces easily with the web (e.g. Java).
Non Coding RNA Web Interface
The discovery of novel non-coding RNAs has been among the most exciting recent developments in Biology. Yet, many more remain undiscovered. We have developed a new software, FastR, to solve following problem: Given an RNA sequence with a known secondary structure, efficiently compute all structural homologs (computed as a function of sequence and structural similarity) in a genomic database.
We would like to produce a web server for our program. Users will upload the Stockholm file for the Query RNA and the Fasta file for the genomic sequences from the websites. FastR will run it on the server machine, and the results will display on the web or be sent to the users.
We would also ask the user open an account first.
In the future, It would be better keep the genomic database locally. And, ask the user select the related genomic sequences.
Required: Experience with web programming, Perl programming, C++.
Promoter Modeling in Bacteria and Yeast
A promoter is a collection of binding sites or locations where transciption factors bind to DNA which regulate transcription. The promoter can be thought of as a logical circuit that defines how a gene functions. The logic of the circuit is encoded in the layout of the elements of the promoter. This project will develop a system and statistical framework for the discovery of the parts and modeling of promoters leveraging several previous works on identifying the structure of the promoter. One of the key techniques use will be comparative genomics where many different related bacteria and yeast genomes will be used to discover functional parts of the promoters.
Strategies for comparing GC-biased genomic sequences
Most of the current genome comparison algorithms are designed for comparing DNA sequences with an even distribution over four types of nucleotides. For example, as a typical fast seed-extension alsorithm, BLAST (and other BLAST variants, e.g. BLASTZ, MEGABLAST) design the seed with a normal hashing function without considering special background nucleotide distribution. However, there are some organisms adopt very biased GC content, e. g. Dictyostelium discoideumi with GC-content about 80%.
We want to devise new strategies to compare the sequences from such organism. The potential applications include: (1) the overlap detection phase in fragment assembly of such genome; (2) compare EST (Expressed Sequence Tag) sequences with the genomic sequences; (3) BLAST-like genomic searching; (4) genome-genome comparison.
Requirements: Experience with programming with C/C++
http://cseweb.ucsd.edu/~eeskin/projects/
http://ieb.uni-muenster.de/data/bioinf/teaching/courses/projects/
http://www.poly.edu/sites/polyproto.poly.edu/files/Guided_Studies_BI7583_Szeto_0.pdf
http://merced.jgi-psf.org/gs2/report/
http://www.mquter.qut.edu.au/bio/BioStudentProjects.aspx#VisualAnalysisTools
http://compbio.ucdenver.edu/hunter/bioi7713/index.html
http://www.ebi.ac.uk/Rebholz/students.html
http://www.bioinformatics-india.com/new/?q=node/1728
http://www.google.com.pk/search?hl=en&ei=hcLTTLutA8G3cbrTpesE&q=bioinformatics+student+projects&start=10&sa=N
Tumor cells frequently have abnormal genomes. Gain and loss of whole chromosomes, duplications, deletions, translocations, inversions, and other chromosomal aberrations are common. Recent advances in sequencing technology allow us to obtain high-resolution, genome-wide information about these changes. However, the interpretation of this data requires the development of visualization tools. This project will develop such tools and use these tools to test various hypotheses about tumor genome architecture.
Required: Experience with graphics programming, preferably in a language that interfaces easily with the web (e.g. Java).
Non Coding RNA Web Interface
The discovery of novel non-coding RNAs has been among the most exciting recent developments in Biology. Yet, many more remain undiscovered. We have developed a new software, FastR, to solve following problem: Given an RNA sequence with a known secondary structure, efficiently compute all structural homologs (computed as a function of sequence and structural similarity) in a genomic database.
We would like to produce a web server for our program. Users will upload the Stockholm file for the Query RNA and the Fasta file for the genomic sequences from the websites. FastR will run it on the server machine, and the results will display on the web or be sent to the users.
We would also ask the user open an account first.
In the future, It would be better keep the genomic database locally. And, ask the user select the related genomic sequences.
Required: Experience with web programming, Perl programming, C++.
Promoter Modeling in Bacteria and Yeast
A promoter is a collection of binding sites or locations where transciption factors bind to DNA which regulate transcription. The promoter can be thought of as a logical circuit that defines how a gene functions. The logic of the circuit is encoded in the layout of the elements of the promoter. This project will develop a system and statistical framework for the discovery of the parts and modeling of promoters leveraging several previous works on identifying the structure of the promoter. One of the key techniques use will be comparative genomics where many different related bacteria and yeast genomes will be used to discover functional parts of the promoters.
Strategies for comparing GC-biased genomic sequences
Most of the current genome comparison algorithms are designed for comparing DNA sequences with an even distribution over four types of nucleotides. For example, as a typical fast seed-extension alsorithm, BLAST (and other BLAST variants, e.g. BLASTZ, MEGABLAST) design the seed with a normal hashing function without considering special background nucleotide distribution. However, there are some organisms adopt very biased GC content, e. g. Dictyostelium discoideumi with GC-content about 80%.
We want to devise new strategies to compare the sequences from such organism. The potential applications include: (1) the overlap detection phase in fragment assembly of such genome; (2) compare EST (Expressed Sequence Tag) sequences with the genomic sequences; (3) BLAST-like genomic searching; (4) genome-genome comparison.
Requirements: Experience with programming with C/C++
http://cseweb.ucsd.edu/~eeskin/projects/
http://ieb.uni-muenster.de/data/bioinf/teaching/courses/projects/
http://www.poly.edu/sites/polyproto.poly.edu/files/Guided_Studies_BI7583_Szeto_0.pdf
http://merced.jgi-psf.org/gs2/report/
http://www.mquter.qut.edu.au/bio/BioStudentProjects.aspx#VisualAnalysisTools
http://compbio.ucdenver.edu/hunter/bioi7713/index.html
http://www.ebi.ac.uk/Rebholz/students.html
http://www.bioinformatics-india.com/new/?q=node/1728
http://www.google.com.pk/search?hl=en&ei=hcLTTLutA8G3cbrTpesE&q=bioinformatics+student+projects&start=10&sa=N
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