v1.0.0
SDRAP - Scrambled DNA Rearrangement Annotation Protocol
Github & documentation
Errors:
Annotate
Output
MySQL database
Hostname
(error)
Username
(error)
Password
(error)
Database name
(error)
Organism information
Genus
(error)
Species
(error)
Strain
(error)
Taxonomy id
(error)
Genome assemblies
Precursor genome
OXY_MIC_sample.fna
NC_000017.11_ERBB2.fna
skbr3_top100.fa
Oxytricha_trifallax_micronuclear_assembly.fasta
oxytri_mic.fna
Precursor sequence description delimiter
(error)
Product genome
Oxytricha_trifallax_022112_assembly_sample.fasta
skbr3.falcon.pa_ctg.fa
skbr3_top100.fa
NC_000017.11_ERBB2.fna
O_trifallax_2020.assembly.unique.fasta
Product sequence description delimiter
(error)
Telomere motif
(error)
Telomere detection
Max relative error
(error)
Max cumulative error
(error)
Max length
(error)
Max offset
(error)
Min length
(error)
Alignment merging
Max shift
(error)
Max distance
(error)
Preliminary annotation
Min alignment length
(error)
Min alignment bitscore
(error)
Min alignment percent identity
(error)
Min alignment coverage contribution
(error)
Additional annotation
Min alignment bitscore
(error)
Min alignment percent identity
(error)
Min product interval coverage for matches
(error)
Min product interval coverage for fragments
(error)
Augmenting annotation
Min gap length
(error)
Compute pointers
(error)
Min pointer length
(error)
Compute match-complementary regions
(error)
Min match-complementary region length
(error)
Property computation
Min coverage
(error)
Max overlap tolerance
(error)
Unambiguous subarrangement limit
(error)
Complete
(error)
Consecutive
(error)
Ordered
(error)
Output parameters
Min coverage
(error)
Use SDRAP aliases
(error)
Output gaps
(error)
Output fragments
(error)
Output summary
(error)
Creating Database:
Creating Database
Database Created!
Error Creating Database!
Uploading Assemblies and Annotating Telomeres:
Uploading
Assemblies Uploaded and Product Telomeres Annotated!
Error Uploading Assemblies or Annotating Telomeres!
Running BLAST+ on Precursor and Product Assemblies and Uploading HSPs:
BLASTing
High Scoring Pairs Identified and Uploaded!
Error Finding or Uploading High Scoring Pairs!
Annotating Matches, Gaps and Pointers and Computing Coverage:
Annotating
Matches, Gaps and Pointers Annotated, and Coverage Computed!
Error Annotating Matches, Gaps or Pointers, or Computing Coverage!
Computing Properties:
Computing
Properties Computed!
Error Computing Properties!
Outputting Data:
Outputting
Data Output!
Error Outputting Data!