Xiaowei's Computer Programs
Bioinformatics Tools
PrimerBank is a free online database for PCR primers designed for gene expression detection or quantification. PrimerBank contains about 150,000 primers covering most known human and mouse genes.
OligoPicker selects up to five oligo probes for each of the DNA sequences you provide for microarray printing. OligoPicker picks specific oligos by skipping regions with contiguous bases common in other sequences. In addition, oligo specificity is double-checked by BLAST.
The
MGH-PGA Proteomic Database
The MGH-PGA Proteomic Database is based on NCBI's protein database, with the additional information about coding DNA sequences. Our database was constructed by parsing the human and mouse GenPept release from NCBI. The corresponding DNA coding regions were then retrieved from GenBank via the CDS feature and were included in our database.
With our database, you can do:
Database Search for GenBank gene accession number, protein ID, GI, keyword, DNA sequence or peptide sequence One of the best features of our database is that you could easily identify the corresponding DNA coding sequences by searching for peptide sequences.
Batch DNA Sequence Retrieval Once you have a list of peptide sequences in FASTA format, you may upload the file and get the corresponding DNA coding sequences and other GenBank features. 5' and 3' primers will also be designed for PCR of the DNA coding regions.
Primer
Design -- for an input DNA sequence, both 5' and 3' primers are
designed with a specified melting temperature (Tm).
Oligo
Calculator -- to calculate Tm, GC%, etc for a given oligo.
BioStats --- a statistical program to perform biological data analysis.
Informatics Projects
The
automated online ordering system for MGH DNA Core Facility.
This is similar to other E-commerce web sites. Once you create your user account, you may order oligos with a single click, view and edit your profile, or track your orders. On the other end, the order is automatically processed and is ready to go to the synthesizer. A master bill is generated automatically at the end of each month. The bill manager is also able to control the database via a java-based UI program.
The
Homepage for MGH DNA Core Facility.
Fun Program
U.S.
President Search - A versatile search box for information about all U.S.
presidents.