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Tour: viewMultiTCW
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viewMultiTCW
Overview | Cluster Table | Pairs Table | Sequence Table | Alignment | Filters

viewMultiTCW displays information from a multiTCW (mTCW) database, which was created by one or more singleTCW (sTCW) databases. A sTCW database can be created from nucleotide (NT-sTCW) or protein (AA-sTCW) sequences. A mTCW database created only from NT-sTCW databases contains both nucleotide sequences and the corresponding translated ORFs, and special statistics on the coding regions, e.g. Ka/Ks from the KaKs_calculator1.

1. Overview

Scrolling down in the overview shows the statistics summary, and the Explain button explains how each value was computed.

There are three types of tables: clusters, pairs, and sequences. The tables can be very big, so the top three tabs on the left provide Sample tables of just a few 1000's. All three table types have Filters, which limits the number of rows that are displayed.

The types of clusters in a table depends on how the database was built (see runMulti) for detail. This mTCW database has 6 different types of clusters, as described in the Overview on the right.

2. Cluster Table

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The table on the right was created with the filter to show the clusters of method 'CL-Closure' with at least one sequence for each dataset.

Select a row followed by:

  1. Sequences: the table of sequences for the cluster will be shown (see lower left image). The columns Ww, Xx, Yy, Zz are the RPKM values.
  2. Pairs: the table of pairs for the cluster will be shown (see lower right image). Only pairs that share a blast hit will be in the database. Only two of these pairs has a PCC>0.8, which is the correlation between the RPKM values in the sequence table.
Sequences: Sequences in selected cluster Pairs: Pairs in selected cluster

3. Pairs Table

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Selecting a row followed by Sequences creates a table of two sequences; from the sequence table, you can see how they align.

The figure on the right shows the columns for pairs. All 3 types of table work as follows:

  1. The Select Column panel displays all possible columns.
  2. Mousing over a column describes it in the lower left.
  3. Selecting or deselecting a column name immediately shows or removes the column from the table.
  4. The columns can be sorted and moved around.
All three tables also has a "Show Column Stats" option to display summary statistics for the rows and numeric columns of the displayed table, as illustrated on the right (results from the Pair Table displayed above).

4. Sequence Table

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Align:
  1. NT and AA: all selected sequences will be pairwise aligned using dynamic programming.
  2. Pairs: only two sequences can be selected and they are aligned by AA, CDS and NT.
  3. MUSCLE: either the cluster or selected sequences will be aligned using MUSCLE3.
  4. MAFFT: either the cluster or selected sequences will be aligned using MAFFT4.

5. Alignments

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MUSCLE alignment of a cluster (MUSCLE is only available on desktops, but pairwise is available from the web applet).


AA, CDS and NT alignments of a pair. The text alignment can be viewed by clicking the AA, CDS or NT buttons.


Menu for the CDS text alignment: Text alignment of the CDS showing matches. The '|' are mutations in synonymous codons, the '*' in nonsynonymous codons.

6. Filters

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Cluster Filter
Pair Filter
Sequence Filter
Pair Filter (continue)

References

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  1. Zhang Z, Li J, Xiao-Qian Z, Wang J, Wong, G, Yu J (2006) KaKs_Calculator: Calculating Ka and Ks through model selection and model averaging. Geno. Prot. Bioinfo. Vol 4 No 4. 259-263.
  2. Li L, Stoeckert CJ, Jr., Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
  3. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
  4. Katoh K, Standley DM (2013) MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution Vol 30, Issue 4 772:780
Email Comments To: tcw@agcol.arizona.edu