MICR/MBMB460

Computers and Bioinformatics

Below are just a few of the many bioinformatic databases available on-line

National Center for Biotechnology Information (NCBI): Resource for molecular biology information

Basic Local Alignment Search Tool (BLAST): Finds regions of similarity between biological sequences

• blastn: searches the nucleotide database with a nucleotide query
• blastp: searches the protein database with a protein query
• blastx: searches the protein database with a translated query
• tblastn: searches the translated nucleotide database with a protein query
• tblastp: searches the translated nucleotide database with a translated query

NCBI-MicrobialGenomes

Microbes Online: A website for browsing and comparing bacterial genomes

BacMap: Bacterial genome atlas

Phage Database:

IslandPath: Helps predict pathogenicity islands

Ribosomal Database Project (RDP)

Comprehensive Microbial Resource: Genome analysis as well as downloading sequences according to genome coordinates

Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA): Metagenomics

Meta Genome Rapid Annotating using System Technology (MG-RAST): Metagenomics through 'The SEED' database

Sequences that will be used in class for analysis:

#1)

AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGGATGAAAGGAGCTTGCTCCTGGATTCAGCGGCGGACGGGTGAGTAATGCCTAGGAATCTGCCTGGTAGTGGGGGACAACGTTTCGAAAGGAACGCTAATACCGCATACGTCCTACGGGAGAAAGCAGGGGACCTTCGGGCCTTGCGCTATCAGATGAGCCTAGGTCGGATTAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCCGTAACTGGTCTGAGAGGATGATCAGTCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGTTGTAGATTAATACTCTGCAATTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCCGCCGCGGTAA

_#2)

_{MKKIKIVPLILIVVVVGFGIYFYASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEV}

_{EMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKED}

_{GMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSK}

_{KDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETES}

_{RNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVT}

_{IVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLAL}

_{VSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLD}

_{DKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFE}

_{KGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALEN}

_{NGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGT}

_{AELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENG}

_NKKYDIDE

_{#3) CGCTGGGGCTCGACCTGCACGCGCCCTACTTCCGGACCGTCGAATCCTATGACAACGACGGCAGGATCTTCGAGCGGATCGTCATCGAGAAGATCGCGCCGGCCCCGCTCGACGAATCCGCGTTCGACCCGAAAAACCCGGACTACGCGTTCTGAGCGTCAACAGCGTGCCGCGTGTCGCGCTCAGTCGTCGTCATCGTCGTGATGATGCTTGTGCCAACGCTTGTAATAGTGCTTGCGCCATTTCCGGTAACGGTCGTCGTCCTCGTCGCCGTCGTAACCGTATCCGTAGCCCGGATACGCGACCACCGCCGGCTGCGGCGCCACATAGACCGGCGCCGGTTCGACATAGACCGGCGCGACCGGCACGCCGACGCCCACCGACAGGTCGACGTGCGCCATTGCACTGGCGGAAGCGAGCAGCGCCACGCTCCCGATCGATACCGCCCATCCCCTCTTGTTCATGTTTCCGTTCCCTGATCCGCCGGCCTGCCCGGCACGCGCGATGAAGATAAGCCGGCCGCGCCGGGCCAGGTGCTACGCCGCTGCGAGAGTCGTAACGCGACGTAACGAAACGGCGTTCGCCATTTGGCCGAATCGCGAAAACGCGCTGGACCGTCTATAGTGGGTTACGGTTCGACACAATCACGAGCGCGCGCTGCTGGAACGAACAGGGTAAAATCCCGCCAAACACTTGGTGGGCGACCACGCCATCCACACGCACAACATATTCTCTGACGCAGGCTCCTGCCGCACCTCAATGGCCAATCCCGCAGAATCCCATCCGCAAAACGACTTCATCAATTCGGCGCGCAAGGAACGTAAGCGTGTTGAAATCTATCTCGTCAACGGCATTCGTCTGACGGGGTGTATCGAGTCGTTCGACCAGTACCTGGTGATGCTGCGCACCCCCGTGGGTCTGCAAGGCATCTACAAGCGTGCGATTTCCACGATCCAGCTCGATACGGGCGGCTCGCGCCCGGGCGGCGGCGGCCCCCGCGGCCCGCGCACCGGCGGTCGGCCGGGCGGCCGCGAAGGCGGCGGTCACAGCCCGTACGGCTCGCACGGCGGCTCCCGCGAATCCCGCGGCGACGGCGGCTACGGCTCGCGCGAGCCGCGTGAAGGCTACGGCTCCCGTGAACCGCGCGAAGGCTATGGCTCCCGCGAACCGCGCGAGGGTTATGGCGCGCCCCGCGAGGGTTACAGCGCTCCGCGTGAACCGCGTGAAGGCTACAGCGCGCCGCGCGACACCGGCGACGCATCGGGCAGCACGTCGCCGTCCGATACCCGCGGCGGCAACGGGCCGGTGATCGTCACGCGCCGCCGGCGAATCGTGCCGGACGGCCAGTAAGACAAAAGGGCAAGCCAACCGGCTTGCCCTTTTTCCTGGTGAGCCGGCGCGGCATGTCGCCGCACCGGCCGTACCGTGATCGCTCAGTGTGCCGTCGCCGGCAAGCCCGCGTTGGCCTCGCGCTGCAGCGAACGCACCTGCTGCTGCAATGCGCGCAGTTGCGACTGAAGCTCCGCCTGTTGCGCCTGCAGCGCCGCCGTTTCATTGCGGACGCTCTTCTGGCGATCCACGACCGCGGCCTGCTGCTCGCGTGCGATGGAGATGTCGGCCTGCAGACGCCGCGCCCGCTCCTGCGTGAGCGCGATCTGCCGGTCCGTCTGTGCCTTCTGCGATTCCAGCTTCGCCGCACGCAATTCGTTGACGGCCAGCCGTTCCGCCTGATGCGAGAAATCGCGATAGATCGCTTCCGCCCGCGTTTCGTCGTAACTCTTGATCACGCGCCAGAACGCCTTCTGCTGGAACAGCGCGACGAAATAGGCACCGTCCTTCACGCTGAACAGCAGGCTCGCGCCGTAGCTGCCGTTATAGCTCGTGCGCATTTCCGTCAGCGAATGCGCCTGAATCTGGCGCTGCAGCTCGTCAACCGTGCTCGGCCCGGTCGTGTCGCCCGCCTGCGGCTGCACCGACGTTTGCACCTGCTGGTCCAGCACCGGAATCGCCGCCACCGGCGCCGACGCCTGCTGGACCGCCGGCGCTCCATTGCCGGCCAGCCCCTGCGCGTACGCGCCCTGCACGCCTCCCATCATCGCGAGCAACACACACGCCCGCGCCAACCCCGTCATATGGCTCATGAATTTTTATTCCCCGCCCGTATCGTTGTAATGCAGCGCGATTTTATCTCATTAATTATTCGCTTTCGCGGGTCTCGGGCTCTTCGTCGAATATCTGATACTTGCGCATCTTTTCCCATAACACCTTGCGGCTGATGCC}