For Wednesday:

• Bring at least one question to class for discussion/review (check the take home exams for things that aren't clear to you).

For Friday:

Review gene and genome rearrangements.

• How would a misplaced origin of replication look like if two similar genomes are compared in a gene plot?
• Which part of a circular bacterial genome is least conserved?
• How would an inversion inside a protein coding gene look like in dotlet? (If you compare the two proteins? If you compare one protein to the encoding DNA sequence?)
• How would a large inversion look like in a gene plot?
• Check today's slides for example on genome rearrangment.

• Read through taxplot info below
• Bring user numbers and passwords for cluster
• PLEASE, fill out the online class evaluation! (Thank you to the 5 students that did already.)

For Today:

• Think about project for which one could use PSI-blast or Hmmer searches.
• Questions on Takehome Exam #9

Any additional question regarding selection and the modern synthesis, or selection and evolution of modern humans.

Questions on PSI Blast?

When is using PSI blast on a nucleotide databank an advantage?

Slides for today (PSI blast, HGT, tardigrades, supertrees and supermatrix approaches).

Other Genome comparison TOOLS at the NCBI   In an attempt to capture some phylogenetic information in blast comparisons, Olendzenski et al. pioneered an approach to use multiple reference genomes to screen for putatively horizontally transferred genes (see Fig. 4). A similar approach, but using only two instead of three reference genomes is implemented in the TAX PLOT program at the NCBI's genome page (see below). You pick one genome to analyze, and two reference genomes. The program returns a plot of every ORF in the selected genome represented in a coordinate system, where the two coordinates are the highest alignment score with the two reference genomes: Selected genome was from Borrelia burgdorferi. The list of selected genes is below: Definition Blast2Seq GenBank Blink V-type ATPase, subunit B (atpB) [Borrelia burgdorferi] 15594439 => aa V-TYPE ATP SYNTHASE BETA CHAIN (V-TYPE A 722 12585403 => aa ATP synthase F1 alpha subunit [Aquifex a 261 15606090 => V-type ATPase, subunit A (atpA) [Borrelia burgdorferi] 15594440 => aa H+-transporting ATP synthase, subunit A 1051 11498766 => aa ATP synthase F1 beta subunit [Aquifex ae 221 15607015 => prolyl-tRNA synthetase (proS) [Borrelia burgdorferi] 15594747 => aa prolyl-tRNA synthetase (proS) [Archaeogl 655 11499201 => aa proline-tRNA synthetase [Aquifex aeolicu 167 15605873 => phenylalanyl-tRNA synthetase, beta subunit (pheT) [Borrelia burgdorferi] 15594859 => aa phenylalanyl-tRNA synthetase, subunit be 709 11499019 => aa phenylalanyl-tRNA synthetase beta subuni 153 15606806 => chemotaxis histidine kinase (cheA-1) [Borrelia burgdorferi] 15594912 => aa chemotaxis histidine kinase (cheA) [Arch 798 11498645 => aa histidine kinase sensor protein [Aquifex 86 15605839 => methionyl-tRNA synthetase (metG) [Borrelia burgdorferi] 15594932 => aa methionyl-tRNA synthetase (metS) [Archae 873 11499048 => aa methionyl-tRNA synthetase alpha subunit 436 15606482 => spermidine/putrescine ABC transporter, ATP-binding protein (potA) [Borrelia burgdorferi] 15594987 => aa spermidine/putrescine ABC transporter, A 678 11499200 => aa ABC transporter [Aquifex aeolicus] 325 15607081 => lysyl-tRNA synthetase [Borrelia burgdorferi] 15595004 => aa lysyl-tRNA synthetase (lysS) [Archaeoglo 642 11498815 => aa cysteinyl-tRNA synthetase [Aquifex aeoli 92 15606347 =>

 

Goals class 25:

• Understand how taxplot, or similar approaches (HGT index), can provide preliminary identification of horizontally transferred genes.
• Know about the problems associated with shotgun genome sequencing of multicelluar organisms that live with their symbionts and other bacteria - these genome sequences should be considered metagenome sequences.
• Understand that binning based on composition and coverage can help identify genes from the host and differentiate them form bacterial genes. (But might classify genes recently transferred to the host as belonging to bacteria.)
• Understand the demonstration that the UNC tardigrade genome contigs contained many genes not part of the tardigrade genome.