GSF R1/R2 Data: Heatmaps for (R1/R2) + "Master" Data - 2

• R1 100K + Master 1020 SWG PID Vs. Alignment Length

• Reversed R2 100K + Master 1020 SWG PID Vs. Alignment Length

GSF R1/R2 Data: Heatmaps for (R1/R2) + "Master" Data

• 100K+1020 R1 Reversed Alignment Length Vs Alignment Length

• 100K+1020 R1 Reversed Score Vs Score

• 100K+1020 R2 Reversed Alignment Length Vs Alignment Length

• 100K+1020 R2 Reversed Score Vs Score

GSF R1/R2 Data: Heatmaps for (R1/R2) Data

Heatmaps for corresponding 100k random samples of GSF data.

• R2 SWG PID Vs R1 SWG PID

• R1 SWG PID Vs R1 SWG Align Length -- length cut > 100 on right

• R2 SWG PID Vs R2 SWG Align Length -- length cut > 100 on right

Pairwise Distances from MSA Vs Pairwise Local Alignment Distances for Revised 599Nts

Following heatmap present the correlation between distances computed from multiple sequence alignment (MSA) versus pairwise local alignment for revised 599Nts dataset (MSA is available here and sequence file is here).

Details on MSA based distance computation is at http://salsafungiphy.blogspot.com/2013/06/pairwise-distance-calculation.html

Details on pairwise local alignment based distance computation is at http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html

Pairwise Distances from Multiple Sequence Alignment (MSA) Vs Pairwise Local Alignment Distances

Following heatmaps present the correlation between distances computed from multiple sequence alignment (MSA) versus pairwise local alignment. Distance computation from MSA is explained in the previous post at http://salsafungiphy.blogspot.com/2013/06/pairwise-distance-calculation.html. Distances computed from pairwise local alignment follows the usual recipe of using Smith-Waterman with -16/-4 gap penalties and EDNAFULL scoring matrix for alignment followed by percent identity based distance computation. A similar study was done with previous data as well (see http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html).

• 599Nts data set

• 999Nts data set

Heatmaps of 10D vs 3D vs SWG

Here we list heatmaps of distances resulted from dimensional scaling versus original Smith-Waterman for two datasets. The description of distances is as follows.

• SWG PID
• Percent identity distance calculated from Smith-Waterman local alignment of sequences using EDNAFULL scoring matrix, gap open –16, and gap extension –4. Previous study on SWG PID compared to several other distance measures can be found at http://salsafungiphy.blogspot.com/2012/10/heatmaps-of-different-distances.html
• 10D
• The 10 dimensional Euclidean distance based on DA-SMACOF mapping of SWG PID
• 3D
• The 3 dimensional Euclidean distance based on DA-SMACOF mapping of SWG PID

The two datasets are described at http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html

 

Heatmaps for Fungi 200

 

3D DA-SMACOF of SWG PID Vs SWG PID	10D DA-SMACOF of SWG PID Vs SWG PID
10D DA-SMACOF of SWG PID Vs 3D DA-SMACOF of SWG PID

Heatmaps for Fungi 2133

3D DA-SMACOF of SWG PID Vs SWG PID	10D DA-SMACOF of SWG PID Vs SWG PID
10D DA-SMACOF of SWG PID Vs 3D DA-SMACOF of SWG PID