Analzying sequences, generating phylogenetic trees, and identifying sequences using BLAST

Tools: Biophython, BLAST, matplotlib

Determine statistics on word occurences and Zipf's law

Tools: matplotlib

Investigate and document the relationships between genes, enzymes and pathways

Tools: SQL(sqlite3), pandas, Biopython, entrez

Obtain secondary structures of folded RNA investigate riboswitch scenarios in the paper by Penchovsky and Breaker

Tools: RNAfold

Run bowtie analysis on strains of Shewanella oneidensis, solving contamination and analyzing coverage statistics

Tools: bowtie2, samtools, matplotlib

Investigate compression algorithms on generated binary and fasta files and real biological information

Tools: numpy, matplotlib, gzip, bzip2, pbzip2, ArithmeticCompress, entrez

Assemble genome de novo using PacBio and Illumina reads, extract quality statistics, identify taxonomic origin, and obtain two genome annotations via different pipelines

Tools: spades, assembly-stats, rna_hmm3, bedtools, SeqMatch, BASys, RAST