TopTerm Definitions
3' Trim Position
The base pair position in the raw sequence corresponding to the last base pair in the processed sequence.
Sequence downstream of this base pair in the raw sequence was trimmed to produce the processed sequence.
5' Trim Position
The base pair position in the raw sequence corresponding to the first base pair
in the processed sequence. Sequence upstream of this base pair in the
raw sequence was
trimmed to produce the processed sequence.
Bases from Gene Start
The predicted location of the transposon within the cDNA of a given gene.
Best Blast Hit
Coming soon
BLAST Bit Score
Coming soon
BLAST Bit Score Threshold
Users can select threshold BLAST Bit Score values for a Search. Inputting a minimum value will return mutants with alignments that have a BLAST Bit Score greater than the value entered. Similarly, entering a maximum value will return mutants with alignments that have a BLAST Bit Score less than the entered value.
BLAST Bit Score Separation
The difference between the highest BLAST Bit Score and the second highest BLAST Bit Score for the alignment of a single processed sequence with genomic sequence. A high BLAST Bit Score Separation indicates that the genomic sequence with the highest BLAST Bit Score is clearly adjacent to the transposon insertion site.
Default Offset Location
Coming soon
Extrapolated Insert Location
The predicted location of the transposon insertion. The genome location of the first
aligning base pair minus the number of base pairs in the processed sequence between the first aligning base
and the end of the transposon sequence.
Gene Description
Coming soon
Gene ID
The unique gene number assigned to each predicted PA14 gene by the Ausubel
laboratory during sequencing of the PA14 genome, i.e. GID1234
Gene Name
Annotated name of PA01 genes and their PA14 homologs, i.e. lasR, rhlR, pilA etc.
Gene Length
Coming soon
Gene Start
The genome location of the predicted cDNA start for a given gene.
Gene Stop
The genome location of the predicted cDNA stop for a given gene.
Genome Sequence ID
Coming soon
Genetic Background
See Production Methods page Genetic Backgrounds section.
Genome Location
Location within the PA14 genomic sequence.
Identities
Coming soon
Mutant ID
Unique numbers assigned to every mutant in the PA14 Transposon Insertion Library
PA01 Homolog
Unique numbers assigned to each PA01 gene, i.e. PA1234
PA14NR SET Mutants
Coming soon
PA14NR SET 96-well Plate
Coming soon
PA14NR Set Plate Position
Coming soon
Percent of Processed Sequence That Aligns
Coming soon
Processed Sequence
High quality sequence for a given mutant as determined by the Phred program
(http://www.phrap.com).
Phred assigns a quality score for each base called in each raw sequence.
Low quality bases are trimmed off the raw sequence to produce the processed sequence.
Processed sequences are subjected to BLAST alignment with the PA14 and PA01 genome sequences.
Query Start
The base pair in the processed sequence where the alignment with the genomic sequence begins.
Query End
The base pair in the processed sequence where the alignment with the genomic sequence ends.
Raw Sequence
The sequence retrieved from the abi file generated after sequencing the arbitrary PCR product for a given mutant. Contains all sequence data for a given mutant.
Raw Sequence Start
The extrapolated genome location of the first base in the raw sequence based on the number of
bases in the raw sequence between the first base of the raw sequence and the first base in the raw sequence that aligns.
Sequence Alignment Disruption by ARB Primers
Because arbitrary (ARB) primers have been used to produce the DNA templates for sequencing, the presence of these primers is often evident in the sequence used to identify transposon insertion sites. ARB primer sequences often appear as a stretch of approximately 10-30 Ns embedded in the Raw and/or processed sequence. Sequences upstream and downstream of the ARB Primer sequence will align with genomic sequence as two separate sequences. Because BLAST alignments of mutants with an ARB primer sequence present in the processed sequence are split into two different alignments, the Bit Score for either alignment will not be as high as the Bit Score would be if the ARB Primer was not present. For this reason, alignments with lower Bit Scores often indicate the correct insertion site, as long as the predicted insertion site is the same for both alignments.
Strain
Coming soon
Strand
Coming soon
Subject Start
The genome location where the alignment begins.
Subject End
The genome location where the alignment ends.
Transposon
See Production Methods page Transposons
section and Transposon Mutagenesis and Colony Selection section.
Transposon Sequence Match Quality
The number of mismatches in the alignment of the raw sequence with the actual sequence of the transposon.
Mutant Report Page
Search
TopSearch All Database Fields Page
This search page is similar to Search Database Fields page. The program will search terms you
typed in on fields Gene ID, Gene Name, PAO1 Homolog and
Mutant ID.
You can enter multiple terms separated by comma, semicolon or space.
TopSearch Database Fields Page
TopAdvanced Search Options
Match Type
Exact or Partial
Query Terms
All terms or Any terms
Query Scope
Entire Library or PA14 NR Set only
TopAdvanced BLAST Options
The processed sequence of each mutant has been subjected
to BLAST alignment against the PA14 and PA01 genomic sequences. Because a single
processed sequence can align with more than one location in the
genome (i.e. the entire processed sequences aligns with one location
while a small stretch of the same processed sequence aligns with sequence at a
different genome location), a single processed sequence can align with multiple locations
in the genome. In most cases, (except where gene duplications have occurred) processed sequences
align best (highest Bit Score) with one particular sequence in the genome that represents the true site of the insertion.
This alignment will have a higher bit score than alignments of small fragments of the same processed
sequence with other sequences in the genome. On the other hand, in some cases, the quality of
processed sequences recovered for particular mutants is fairly poor or the
alignments are separated by ARB Primer sequences (see Sequence Alignment Disruption by ARB Primers above). In these cases,
the best genomic sequence alignments for these processed sequences can have relatively low
Bit Scores (Bit Score of ~60), but may represent true transposon insertion sites.
Using the filters below, users can opt to filter lower Bit Score alignments out of a search,
Bit Score Threshold: Users can select threshold Bit Score values for a Search. Inputting a minimum value will
return mutants with alignments that have a Bit Score greater than the value entered. Similarly, entering a maximum
value will return mutants with alignments that have a Bit Score less than the entered value.
TopSearch Genome Locations
Enter genomic coordinates in base pairs (i.e. 10000 to 20000).
Please note that because the PA14 sequence is currently being assembled,
PA14 genomic coordinates will change.
TopSearch PA14NR Set Plate Positions Page
Top
Search Results Page
