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Tour: viewMultiTCW
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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.

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 3 different types of clusters, as described in the Overview on the right.

2. Cluster Table

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The table was created with the filter to show the clusters of method 'CL-Closure' with at least one sequence for both datasets.

Select a row followed by:

  1. Seqs/Align: 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 one of these pairs has a PCC>0.8, which is the correlation between the RPKM values in the sequence table.
Seqs/Align: Sequences in selected cluster Pairs: Pairs in selected cluster

3. Pairs Table

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

For all tables:

  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.

4. Sequence Table

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Align (shown below):
  1. NT Pairs and AA Pairs: all selected sequences will be pairwise aligned using dynamic programming.
  2. MUSCLE: all selected sequences will be aligned using MUSCLE3.
  3. Pairs: only two sequences can be selected and they are aligned by AA, CDs and NT.

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)


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  1. Li L, Stoeckert CJ, Jr., Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
  2. 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.
  3. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
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