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Schmidtea
mediterranea Genome Database
Nomenclature
I.
Nomenclature
a.
contigs: v31.019651
i. v31 assembly
version 3.1
ii. 019651 contig
number padded to 6 digits
b.
genes: mk4.019651.00
i. mk4 maker
run 4
ii. 0196510 contig
number padded to 6 digits
iii. 00 gene
number padded to 2 digits
c.
transcripts: mk4.019651.00.01
i. mk4 maker
run 4
ii. 019651 contig number padded to 6 digits
iii. 00 gene
number padded to 2 digits
iv. 01 transcript
number padded to 2 digits
d.
est contigs: ec1.00159.004
i. ec1 est
contig version 1
ii. 00159 est
contig number padded to 5 digits
iii. 004 number
of reads padded to 3 digits
e.
454 contigs: fc1.08641.005
i. fc1 454
contig version 1
ii. 08641 454
contig number padded to 5 digits
iii. 005 number
of reads padded to 3 digits
II.
Browser Overview (Top to Bottom)
a.
Genome locator: Showing 1.071 kbp from v31.019651,
positions 1 to 10,150
b.
Instruction Panel with search examples.
c.
Search Box
i. Terms
for protein homology (piwi)
ii. Contig
names (v31.019651)
iii. Gene
names (mk4.019651.00)
iv. Use
of wildcards(*) (mk4.0196*)
d.
Data source: Choose which dataset to view (SmedGD v1.0)
e.
Overview Panel
i. Simplified
view of the entire genomic contig.
ii. Red
box indicates the area of the contig which is being viewed in Details panel
(see below). The red box can be
recentered on a different area of the contig by clicking on a new area in the
overview panel. The size of the
box and therefore the number of basepairs viewed in the details panel can be
altered by changing the parameters in the Scroll/Zoom dropdown menu or by
adding the desired region to be viewed in the Search Box of the contig. (v31.019651:1375..2445)
f.
Details Panel
i. Information
that aligns to genome, everything from predicted genes to RNAi phenotype
information.
g.
Tracks
i. The
information in the Details panel is controlled by the selection of tracks.
Tracks are types of information that are generated biologically and bioinformatically
that have been aligned to the genomic contigs.
III.
Tracks
a.
Overview (v31.000001)
i. Viewed
in the Overview panel
ii. HQ
Genes
iii. Maker
Genes
iv. Human
Curated Genes
b.
Analysis
i. Restriction
Sites: maps restriction sites to the genome.
c.
Genes
i. Predicted
Genes/mRNAs with Evidence: This track is composed of genes/mRNAs predicted by
Mark Yandell's Maker that are supported by High Quality evidence, such as est
and protein homology.
ii. Predicted
Genes/mRNAs: Any maker predictions that do not have High Quality evidence as
support are located in this track.
iii. Human
Curated Genes/mRNAs: Any human curated genes/mRNAs. Currently, only genes investigated by Alejandro S‡nchez
Alvarado with Apollo are presented in this track, and are identified by the
three letter designation ASA, followed by a gene number and transcript number (ASA.00084.01).
d.
Phenotype/Expression:
i. cDNA
microarray: All ESTs were aligned
to the genome using blat (see ESTs aligned with Blat). The microarray result associated with a
particular EST is mapped to every alignment of that EST to the genome. A arrow centered on an EST indicates
up- or down-regulation in comparison to the control (green for up, red for
down, gray for no change) of that EST in the experiment listed in the arrow's
label (above the arrow). The
logbase 2 change is displayed below the arrow. (AY066135.Irradiation.TimeCourse.24hr)
ii. RNAi
Phenotype: A bar that spans the
length of the EST that was used to disrupt gene function by RNA intereference
is employed in this track. The
description of the resulting phenotype is located under the bar. (RNAi:AY967490)
iii. in
situ: A track that links to in situ
images of the EST that is aligned to this particular region of the genome. (AY967481:insitu)
e.
Sequence Similarity:
i. 454 contigs aligned
with BLAT: Contigs prepared from 454 sequencing reads were aligned to the
genome using the Blat algorithm and standard psl output. BLAT is designed to
quickly find sequences of 90% and greater a score of 30.
ii. BLASTX Hits: These
are WUBLASTX (nucleotide to protein, via six-frame translation) similarity hits
of genomic sequence, run against reference protein datasets from the genomes of
E. coli, Saccharomyces cerevisiae, Drosophila melanogaster, C. elegans,
platyhelminthes, Ciona intestinalis, mouse and human. Cutoffs of 40% identity
and 1e-5 were used.
iii. BLASTX Exonerate:
These are the outputs from BLASTX Hits alignments of the S. mediterranea genome to
reference protein databases and polished with the splice-site aware algorithm
Exonerate (protein2genome) to align protein to genomic sequences (Comput Appl
Biosci 1997 Aug; 13(4) 477-8. pmid:9283765).
iv. EST BLASTN: These
are contigs of S. mediterranea expressed sequence tags (ESTs) aligned to
the S. mediterranea genome. Cutoffs of 85% identity and 1e-10 were used.
v. EST BLASTN
Exonerate: These are contigs of S. mediterranea expressed sequence
tags (ESTs) aligned to the S. mediterranea genome and polished with Exonerate
(EST2genome) to align spliced DNA sequences to unspliced genomic DNA (Comput
Appl Biosci 1997 Aug; 13(4) 477-8. pmid:9283765).
vi. ESTs aligned with
BLAT: These are all available individual S. mediterranea expressed sequence
tags (ESTs) aligned to the S. mediterranea genome using James Kent's BLAT
program [ http://genome.cse.ucsc.edu/cgi-bin/hgBlat]. This track shows the best
unique location for each EST (1e-95 with at least 45% alignment). Output is in
the WUBLAST format.
vii. Maker predictions
BLASTP to Swissprot: These are alignments of predicted proteins from Maker gene
models against Swissprot. A cutoff of 1e-3 and 40% alignment with
the protein hit was used.
viii.
Maker predictions RPS-BLAST to PFAM domains: These are alignments
of predicted proteins from Maker gene models against PFAM using NCBI RPS-Blast.
A cutoff of 1e-3 and 40% alignment with the protein hit was used.
ix. Maker predictions
RPS-BLAST to SMART domains: These are alignments of predicted proteins from
Maker gene models against SMART using NCBI RPS-Blast. A cutoff of 1e-3
and 40% alignment with the protein hit was used.
x. Repeat Regions:
This tracks shows areas of the genome containing interspersed repeats and low
complexity DNA sequences as identified by RepeatMasker using a S.
mediterranea specific repeat library.
f.
Species TBLASTN
i. C.elegans proteome TBLASTN
against Genome: The C.elegans proteome aligned to the translated S.mediterranea genome. Cutoffs of 1e-3
and 30% alignment with the protein query were
used.
ii. D.mel proteome TBLASTN
against Genome: The D.melanogaster proteome aligned to the translated S.mediterranea genome. Cutoffs of 1e-3
and 30% alignment with the protein query were
used.
iii. Human proteome
TBLASTN against Genome: The H.sapien proteome aligned to the translated S.mediterranea genome. Cutoffs of 1e-3
and 30% alignment with the protein query were
used.
iv. M.mus proteome TBLASTN
against Genome: The M.musculus proteome aligned to the translated S.mediterranea genome. Cutoffs of 1e-3
and 30% alignment with the protein query were
used.
g.
Tools
i. 6-frame
translation: Indicates the translation of sequence in all possible reading
frames of the genomic sequence.
ii. Coding Segments:
This track shows the reading frames of coding segments (also known as
"CDS" features).
iii. DNA/GC Content:
Shows the percentage of GC content along genomic DNA. The S. mediterranea genome is AT rich. If the zoom is set to 100bp, the actual
sequence of the genomic contig can be viewed.
h.
Non-Coding RNA: mapping of mature miRNA sequences (RNA.
2006 Sep;12(9):1640-9. Epub 2006 Jul 18) to the genome with the use of
BLAST (Marc Friedlaender). (sme-miR-2b)
IV.
Display
Settings:
a.
Image
Width
b.
Position
of the Key or track names
V.
Add your own tracks: (help
and more
general help)
VI.
Details Pages and Links
a.
Gene: (mk4.000158.08)
Details about the gene structure (exons, CDS, UTRs), location and sequence.
i. Position:
links back to the browser with a zoomed in view of the gene.
b.
mRNA: (mk4.000158.06.01) Details about the
mRNA structure (exons, CDS, UTRs) and location.
i. Name:
retrieves protein and nucleotide seqeunce.
1.
Links to NCBI Blast and will auto-fill NCBI-Blast form
with the retrieved sequence.
ii. Position:
links back to the browser with a zoomed in view of the mRNA.
c.
miRNA: (sme-miR-2b)
Details
about the mature miRNA length and location.
i. Name:
links to miRBase.
ii. Position:
links back to the browser with a zoomed in view of the miRNA.
d.
cDNA Microarray: (AY066135.Irradiation.TimeCourse.24hr)
Details about log2 ratio, aliases, and position in genome.
i. Position:
links back to the browser with a zoomed view of the EST
e.
RNAi Phenotype: (RNAi:AY967490)
Details about RNAi phenotypes, images, aliases and position in genome.
i. Position:
links back to the browser with a zoomed view of the EST
f.
In Situ: (AY967481:insitu)
Details about aliases, images and position in genome.
i. Position:
links back to the browser with a zoomed view of the EST
g.
Blastn/Exonerate Blastn: (ec1.03089.014)
Details
about the EST alignment to the genome.
i. Name:
retrieves nucleotide sequence of the EST or EST contig
ii. Position:
links back to the browser with a zoomed in view of the EST or EST contig.
iii. Matches:
searches for alignments of this EST/EST contig to other regions of the genome.
h.
ESTs Aligned with Blat: (DQ186986)
Details
about EST aliases and the EST alignment to the genome.
i. Name:
retrieves nucleotide sequence of the EST
ii. Position:
links back to the browser with a zoomed in view of the EST or EST contig.
iii. Matches:
searches for alignments of this EST/EST contig to other regions of the genome.
iv. Target:
links to NCBI
i.
454 contigs Aligned with Blat: (fc1.05410.002)
Details
about the 454 contig alignment to the genome.
i. Name:
retrieves nucleotide sequence of the 454 contig
ii. Position:
links back to the browser with a zoomed in view of the 454 contig.
iii. Matches:
searches for alignments of this 454 contig to other regions of the genome.
j.
Repeat Regions: Details about the repeat and where it is
found in the genome.
i. Position:
links back to the browser with a zoomed in view of the repeat.
ii. Matches:
searches for alignments of this repeat to other regions of the genome.
k.
Blastx/Exonerate Blastx: (gi|52345394|ref|NP_001004365.1|
and ci0100130549)
Details about the protein and the alignment to the genome.
i. Position:
links back to the browser with a zoomed in view of the protein.
ii. Target:
links to the NCBI for all gi numbers and to the JGI for all ci numbers
iii. Matches:
searches for alignments of this protein to other regions of the genome.
l.
Maker predictions RPS-BLAST/BLASTP to
PFAM/SMART/SWISSPROT (mk4.001111.00.01.pfam00069,
mk4.001111.00.01.smart00220,
and mk4.001111.01.01.O08795)
Details about the protein/domain, the location in the genome, and Gene ontology
terms.
i. Position:
links back to the browser with a zoomed in view of the protein.
ii. Target:
links to Pfam/Smart/Swissprot websites.
iii. Matches:
searches for alignments of this protein to other regions of the genome.
m.
Species proteome TBLASTN against S.med Genome: (gi|17538133|ref|NP_496073.1|
gi|48255891|ref|NP_001001329.1|
gi|6679465|ref|NP_032951.1|
gi|7298396|gb|AAF53621.1|
) Details about the protein and the location in the genome.
i. Position:
links back to the browser with a zoomed in view of the protein.
ii. Target:
links to NCBI for all gi numbers.
iii. Matches:
searches for alignments of this protein to other regions of the genome.
iv. Note:
links to FlyBase/WormBase/MouseEnsembl/HumanEntrezGene websites
VII.
Other Tools
a.
Blast
i. blastp/blastn/blastx
against maker protein predicted sequences, maker predicted transcript
sequences, or human curated protein sequences.
b.
Blat
i. Nucleotide
vs genome sequence
ii. Results
link to genome browser
c.
Search
i. Protein
homology
ii. Gene
Ontology
iii. RNAi
phenotypes