HCV Database
HCV sequence database
 



To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.


Explanation of QuickAlign Results

Query Location

If you are using a LANL alignment as your alignment set, your results page will begin with a map of the organism. The location of your query is shown as a small red bar.

sample map of genome

If you are using your own alignment for another organism, this map will not be shown.

 

Summary Table

Below the map a short summary table, colored yellow, appears.

sample summary table

The table shows the query sequence, its length, its location in the genome coordinates of the reference sequence, and the alignment used by QuickAlign. There are three buttons below the table that display three analyses of the alignment. The first two identify and count the variants of your query found in the alignment.

If you are providing your own alignment, your choices will be "Summarize All" and "Summarize by User's Grouping".

Summarize All

Here is the output for the first button, the summary of variants in the alignment regardless of subtype or user grouping.

sample summary output

Summarize By Subtype

Here is a sample of the variants grouped by subtype, with a histogram showing the number of mutations relative to the query.

sample subtype summary output

Find Other Matches

If you are using a LANL alignment, you will see a third button "Find Other Matches", which will search the reference sequence genome or proteome for other matches to your query sequence. QuickAlign has used the best match as the basis for extracting your alignment, but there may be other good matches across the genome that could be of significance if you are examining potential PCR primers. The "Find Other Matches" button also examines the reverse complement of your sequence for matches. Here is the output.

If you are using your own alignment for another organism, this button will not be presented.

sample of other matches output

 

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 Subtype". 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 frequence 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 hcv-info@lanl.gov