TAIR The Arabidopsis (a flowing plant) Information Resource Validating the electropherogram (waveform) elegans (worm) genome database –10įlybase Drosophila (fly) sequence and genetic database SGD Saccharomyces cerevisiae (yeast) Genomic Database PDB Protein Data Bank for protein 3D structure UniProt Universal protein resource (protein sequences) PIR Protein Identification Resource (protein sequences) STS Sequence Tagged Sites (unique DNA sequences used for making maps for human chromosomes) GenBank DNA sequences (Collection of all publicly available DNA sequences) ĮMBL DNA sequences (European Molecular Biology Laboratory – similar to Genbank) ĭDBJ DNA sequences (Japan’s equivalent of Genbank) ĮST Expressed Sequence Tags (cDNA sequences reverse transcribed from mRNA) Here are some examples of nucleotide databases (Zou et. There are also Expresses Sequence Tag databases where the DNA sequence may not be very accurate since they are cDNA derived from mRNA. One of the common searches in these databases is to find homology or similar sequences between organisms. The sequence part contains the DNA sequence. The annotation contains the definition of the molecule, the accession number, a unique number used to identify the molecule, and a CDS, the corresponding protein-coding sequence. The sequence file in the database for the particular molecule contains the annotation and sequence. Examples of these databases are GenBank, PDB database, etc. These also describe the structure and function of the biological molecules. The nucleotide sequences of biological molecules like DNA, RNA, and protein of various organisms are stored in Nucleotide databases. Putting it together using a Bioinformatics Management tool.Finding the Open Reading Frame using ORFFinder.Analyzing cDNA sample using Bioinformatics tools.Part two discusses the steps to prepare a cDNA sample taken from the cDNA library to prepare it to be sequenced. Part one of this series showed the steps to create a cDNA library of random DNA fragments isolated from an organism. Part three talks about the use of bioinformatics tools to perform analysis of the DNA sequence. The clone W418.20 codes for a protein that is similar to acid phosphatase/vanadium-dependent haloperoxidase-related protein. With the help of the vWISE team, I submitted clones W418.20 (Landoltia punctata clone W418.20, 2021) and W417.20 (Landoltia punctata clone W417.20, 2021) to GenBank. It’s being researched as a potential food source and in bioremediation. The duckweed plant grows on the water in lakes and wetlands. We also learned how to determine if the cDNA codes for a protein using the ORF Toolbox and look for similar proteins in other organisms. to compare the sequenced DNA with known sequences stored in online repositories like GenBank. We used bioinformatics tools like BLAST, etc. We learned how to isolate the complementary DNA or cDNA fragments from the duckweed ( Landoltia punctata) plant, using techniques like reverse transcriptase, plasmid vectors, polymerase chain reaction (PCR), gel electrophoresis, etc. I had a wonderful opportunity to learn about DNA sequencing and bioinformatics while attending the virtual nine-week Waksman Institute Summer Experience program.
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