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HIV sequence database



Understanding Results from ADRA

************** Disclaimer ****************** * * * ADRA intended for research use only * * * ********************************************


The output file is described below, explanations are in green

The output begins with a table of the sequence name and its associated properties:

Sequence Namexyz123
Identified gene region(s)Protease, RT
HXB2* positions56 - 479

  • Sequence Name The name supplied by the user or found in the input file
  • Identified Gene Regions The gene region(s) detected by the BLAST search.
  • HXB2* positions The start and end co-ordinates of the submitted sequence aligned against the referent sequence (here HIVHXB2).

Next is a table of the changes found in the sequence relative to the referent:

Table of mutations potentially conferring resistance
Protein

aa change

codon change

fold resist

cross resist

compound

record

Protease

L10I

CTC/ATC

ND

ND

MK-639 (L-735,524,

indinavir)

view

RT

V179D

CTC/ATC

20

R82150 (20)

TIBO R82913

view

Gene region detected

Reference sequence on left (L), aa position in center (10), mutation on right (I)

Reference codon on left, mutation codon on right

Fold change conferred (ND=Not Determined)

Cross resistance to other drugs (fold change)

Drug name

view database entry for this drug

Next is a table of the changes found in the sequence based on ambiguous character mutations that may or may not indicate evolving drug resistance at this position

The program identifies mutations based on ambiguous characters in the nucleotide sequence and searches for potential resistance related mutations based on that position. The table then lists these sites

At the end of the resistance table is shown a summary statement of the drug resistances detected:

This sequence could possibly be associated with a degree of resistance to these drugs, TIBO R82913, P9941, MK-639 (L-735,524), indinavir.

Then comes an alignment:

ALIGNMENT

P delineates the Protease gene region
R delineates the RT gene region
I delineates the Integrase gene region
______________________________


QUERY NUC CCTCAAATCACTCTT TGGCAACGACCCATC GTCACAATAAAAATA GGGGGGCAAGTAAGG GAaGCTCTATTARAT
QUERY PRO : : I : : : : : : I : : : : : : : : V R : : : : X
HXB2 PRO P Q V T L W Q R P L V T I K I G G Q L K E A L L D 25
MUTANTS
* * * * *

-P--P--P--P--P- -P--P--P--P--P- -P--P--P--P--P- -P--P--P--P--P- -P--P--P--P--P-

  • The first line of the alignment (QUERY NUC) shows the sequence presented by the user.
  • User supplied upper and lower case and IUPAC ambiguities are preserved and may lead to untranslatable codons, ambiguities are highlighted in red.

  • The second line (QUERY PRO) shows those positions where the sequence’s translation differs from the referent (in this case HXB2)
  • Untranslatable codons, ambiguities are shown as ‘X’

  • The third line (HXB2 PRO) shows the amino acid sequence of the referent (in this case HXB2)
  • A codon count from the start of the submitted sequence is shown on the end of the line

  • The fourth line (MUTANTS) shows asterisks (‘*’) where the differences occur.
  • Under each block of the alignment are shown a symbol for which gene region the displayed sequence belongs too (here Protease).

If the sequence has an unusually high number of differences from the referent after the alignment the following message may be displayed:

*** The sequence has an unusually high count of mutants, you may need to edit your sequence for better alignment. Alternatively the sequence may be of a different subtype than the referent***

 

Finally a table of ambiguities, untranslatable codons and stop codons is shown:

Frequency of ambiguous characters0.012
Number of untranslatable (X) codons4
Stop codons found in query sequence0

  • This table summarizes the ambiguities in the submitted sequence and how many untranslated codons they result in. A frameshift or a pseudogene may also lead to the detection of stop codons.

last modified: Wed Nov 7 14:42 2007


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

 
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