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HFV Ebola sequence database
 

QuickAlign Results

Query Location

If you are using a LANL alignment as your alignment set, your results page will begin with a gene map. The location of your query is shown as a colored bar. Below are the results from the Sample Input for the Conventional QuickAlign.

sample map of Ebola genome

 

If you are using your own alignment for another organism, the genome map will not be shown, and your choices will be "Summarize All" and "Summarize by User's Grouping".

Summarize All

"Summarize All" shows a summary of the frequency of all unique sequences in the alignment compared to the input sequence.

Summarize By Species

In this summary, variations are grouped by species , with a histogram showing the number of mutations relative to the query.

 

Alignment

QuickAlign presents its alignment result in "output-aligned" format which looks like this.

sample alignment

For ease of reading the alignment is presented in groups of 10 characters, a space, then 10 more characters, etc. up to a maximum line width of 50 characters. If the query is longer than 50 characters, it will be continued below.

Wide Output Option

You can force the lines to be longer than 50 characters, by checking "Yes" in the "Display Wide Output" option on the input page. Sequences identical to the query are highlighted in red. You can download a copy of this alignment in a variety of formats by using the scrolling menu and Download button at the top of the alignment.

Calculate frequency by position

On the Results page, you will see buttons for "Summarize All" and "Summarize by species ". If you have selected "Calculate frequency by position" as an option, these summaries will include data showing the frequency of each nucleotide or amino acid at each position.

PositionPercentage and raw
count of non-gap
Non-gap/total
(percentage)
Gap/total
(percentage)
1A: 85.39% (1444)   T: 14.55% (246)   G: 0.06% (1)   1691/1693 (99.88%)2/1693 (0.12%)
2T: 99.29% (1680)   other: 0.71% (12) 1692/1693 (99.94%)1/1693 (0.06%)
3G: 98.11% (1660)   other: 1.89% (32) 1692/1693 (99.94%)1/1693 (0.06%)
4A: 99.70% (1688)   other: 0.30% (5) 1693/1693 (100.00%)0/1693 (0.00%)
5A: 85.82% (1452)   C: 6.97% (118)   G: 3.90% (66)   T: 3.31% (56)   1692/1693 (99.94%)1/1693 (0.06%)
6A: 94.62% (1600)   T: 4.67% (79)   other: 0.71% (12) 1691/1693 (99.88%)2/1693 (0.12%)
7G: 92.96% (1571)   A: 3.96% (67)   other: 3.08% (52) 1690/1693 (99.82%)3/1693 (0.18%)
8C: 83.04% (1405)   T: 16.25% (275)   other: 0.71% (12) 1692/1693 (99.94%)1/1693 (0.06%)
9A: 80.20% (1357)   C: 17.85% (302)   other: 1.95% (33) 1692/1693 (99.94%)1/1693 (0.06%)
10G: 55.08% (932)   C: 25.41% (430)   A: 15.25% (258)   T: 4.26% (72)   1692/1693 (99.94%)1/1693 (0.06%)
11A: 36.98% (626)   T: 31.78% (538)   G: 29.12% (493)   C: 2.13% (36)   1693/1693 (100.00%)0/1693 (0.00%)
12C: 79.55% (1346)   A: 20.09% (340)   other: 0.35% (6) 1692/1693 (99.94%)1/1693 (0.06%)

If "Calculate frequency by position" is selected, the Summarize pages will also contain links to "See full raw counts", which will show you the full residue counts without applying any cutoff.

Pos	A	C	G	T	Weight (% non-gap)

1	1444	0	1	246	0.998818665092
2	0	11	1	1680	0.999409332546
3	3	29	1660	0	0.999409332546
4	1688	2	3	0	1.0
5	1452	118	66	56	0.999409332546
6	1600	7	5	79	0.998818665092
7	67	46	1571	6	0.998227997637
8	11	1405	1	275	0.999409332546
9	1357	302	21	12	0.999409332546
10	258	430	932	72	0.999409332546
11	626	36	493	538	1.0
12	340	1346	5	1	0.999409332546

Below the frequency table is a Sequence Logo (frequency graph) that shows a visual representation the frequency of each residue at each position. The height of letters indicates the relative frequency of each residue at each position. The width of a stack of letters is proportional to the fraction of valid residues in that position, i.e., columns with many gaps or unknown residues are narrow. These graphs are produced by WebLogo 3.

sample weblogo graphic

Multiple Queries

If you submitted multiple query sequences, the output is slightly different. Only one map is presented that marks the location of each of your sequences. Multiple yellow summary tables are shown together. All the alignments are grouped at the end. There is a link that allows you to jump from the summary table to its corresponding alignment.

Links

 




Questions or comments? Contact us at hfv-info@lanl.gov