For Friday

Review gene and genome rearrangements.

For today:

Review session

If out of questions go here for slides.


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 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 =>