#!UGENE_WORKFLOW # workflow "New schema"{ read-sequence { type:read-sequence; name:"Read sequence"; merge-gap:10; mode:0; } filter-annotations { type:filter-annotations; name:"Filter annotations by name"; accept-or-filter:true; } extract-annotated-sequence { type:extract-annotated-sequence; name:"Get sequences by annotations"; complement:true; extend-left:0; extend-right:0; merge-gap-length:1; translate:false; } query { type:query; name:"Annotate with UQL"; merge:false; offset:0; } write-fasta { type:write-fasta; name:"Write FASTA"; accumulate:true; write-mode:2; } sequences-to-msa { type:sequences-to-msa; name:"Join sequences into alignment"; } muscle { type:muscle; name:"Align with MUSCLE"; max-iterations:-1; mode:0; range:"Whole alignment"; stable:true; } write-clustalw { type:write-clustalw; name:"Write ClustalW"; write-mode:2; } query.annotations->filter-annotations.in-annotations.annotations filter-annotations.annotations->extract-annotated-sequence.in-sequence.annotations read-sequence.sequence->extract-annotated-sequence.in-sequence.sequence read-sequence.sequence->query.in-sequence.sequence read-sequence.url->write-fasta.in-sequence.fasta-header extract-annotated-sequence.sequence->write-fasta.in-sequence.sequence extract-annotated-sequence.sequence->sequences-to-msa.in-sequence.sequence sequences-to-msa.msa->muscle.in-msa.msa muscle.msa->write-clustalw.in-msa.msa .iteration "Default iteration"{ id:28; filter-annotations { annotation-names:Mitochondrion; } write-clustalw { } } .meta { visual { read-sequence { description:"

Read sequence

Reads sequence(s) from unset.

"; tooltip:"Reads sequences and annotations if any from local or remote files."; pos:"-945 -600"; style:ext; bg-color-ext:"0 128 128 64"; out-sequence.angle:360; } filter-annotations { description:"

Filter annotations by name

Filters annotations by name.

"; tooltip:"Filters annotations by name"; pos:"-600 -600"; style:ext; bg-color-ext:"0 128 128 64"; in-annotations.angle:180; out-annotations.angle:360; } extract-annotated-sequence { description:"

Get sequences by annotations

Extract each annotated sequence region from Read sequence make it reverse-complement if annotation is located on complement strand.

"; tooltip:"Creates sequences from annotated regions of input sequence"; pos:"-435 -600"; style:ext; bg-color-ext:"0 128 128 64"; in-sequence.angle:180; out-sequence.angle:360; } query { description:"

Annotate with UQL

Analyze each nucleotide sequence from Read sequence with unset.

"; tooltip:"Analyzes a nucleotide sequence using different algorithms (Repeat finder, ORF finder, etc.) imposing constraints on the positional relationship of the results."; pos:"-795 -600"; style:ext; bg-color-ext:"0 128 128 64"; in-sequence.angle:180; out-annotations.angle:360; } write-fasta { description:"

Write FASTA

Writes sequence(s) from Get sequences by annotations in FASTA format to unset.

"; tooltip:"Writes all supplied sequences to file(s) in FASTA format."; pos:"-180 -495"; style:ext; bg-color-ext:"0 128 128 64"; in-sequence.angle:180; } sequences-to-msa { description:"

Join sequences into alignment

Creates multiple sequence alignment from supplied sequences.

"; tooltip:"Creates multiple sequence alignment from sequences."; pos:"-900 -300"; style:ext; bg-color-ext:"0 128 128 64"; in-sequence.angle:180; out-msa.angle:360; } muscle { description:"

Align with MUSCLE

Aligns each MSA supplied with MUSCLE using "MUSCLE default" mode.

"; tooltip:"MUSCLE is public domain multiple alignment software for protein and nucleotide sequences.

MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.

"; pos:"-585 -300"; style:ext; bg-color-ext:"0 128 128 64"; in-msa.angle:180; out-msa.angle:360; } write-clustalw { description:"

Write ClustalW

Save all MSAs from Align with MUSCLE to unset.

"; tooltip:"Writes all supplied alignments to file(s) in CLUSTALW format."; pos:"-270 -300"; style:ext; bg-color-ext:"0 128 128 64"; in-msa.angle:180; } read-sequence.out-sequence->query.in-sequence { text-pos:"-37 -74"; } query.out-annotations->filter-annotations.in-annotations { text-pos:"-49 -78"; } filter-annotations.out-annotations->extract-annotated-sequence.in-sequence { text-pos:"-24 -80"; } extract-annotated-sequence.out-sequence->write-fasta.in-sequence { text-pos:"-47 -86"; } extract-annotated-sequence.out-sequence->sequences-to-msa.in-sequence { text-pos:"-45 -43"; } sequences-to-msa.out-msa->muscle.in-msa { text-pos:"-45 -43"; } muscle.out-msa->write-clustalw.in-msa { text-pos:"-45 -59"; } } } }