Sequence operation utilities

Sequence search tools and sequence operation tools Sequence search tools and sequence operation tools Copyright © [email protected] 2014

Module AssemblyName: file:///D:/GCModeller/GCModeller/bin/seqtools.exe Root namespace: seqtools.Utilities

If you are having trouble debugging this Error, first read the best practices tutorial for helpful tips that address many common problems:

https://github.com/smrucc/gcmodeller/src/analysis/

The debugging facility Is helpful To figure out what's happening under the hood:

http://gcmodeller.org

If you're still stumped, you can try get help from author directly from E-mail:

[email protected]

All of the command that available in this program has been list below:

Tools command that works around the fasta format data.

Tools command that using for finding Palindrome sites.

Prototype: seqtools.Utilities::Int32 Align2(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /align /query <query.fasta> /subject <subject.fasta> [/blosum <matrix.txt> /out <out.xml>]

seqtools

Prototype: seqtools.Utilities::Int32 CheckHeaders(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /check.attrs /in <in.fasta> /n <attrs.count> [/all]

seqtools

Prototype: seqtools.Utilities::Int32 CutMlAlignment(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Clustal.Cut /in <in.fasta> [/left 0.1 /right 0.1 /out <out.fasta>]

seqtools

Prototype: seqtools.Utilities::Int32 CompareFile(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Compare.By.Locis /file1 <file1.fasta> /file2 </file2.fasta>

seqtools

Distinct fasta sequence by sequence content. Prototype: seqtools.Utilities::Int32 Distinct(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Distinct /in <in.fasta> [/out <out.fasta> /by_Uid <uid_regexp>]

seqtools

Prototype: seqtools.Utilities::Int32 GetSimpleSegments(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Get.Locis /in <locis.csv> /nt <genome.nt.fasta> [/out <outDIR>]

seqtools

Prototype: seqtools.Utilities::Int32 GffSites(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Gff.Sites /fna <genomic.fna> /gff <genome.gff> [/out <out.fasta>]

seqtools

Prototype: seqtools.Utilities::Int32 gwANI(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /gwANI /in <in.fasta> [/fast /out <out.Csv>]

seqtools

Testing Prototype: seqtools.Utilities::Int32 LociDescript(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Loci.describ /ptt <genome-context.ptt> [/test <loci:randomize> /complement /unstrand]

seqtools

• Drawing the sequence logo from the clustal alignment result. Prototype: seqtools.Utilities::Int32 SequenceLogo(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /logo /in <clustal.fasta> [/out <out.png> /title ""]

seqtools

The file path of the clustal output fasta file.

The output sequence logo image file path. default is the same name as the input fasta sequence file.

The display title on the sequence logo, default is using the fasta file name.

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaFile Example:

[
    
]

Only search for 1 level folder, dit not search receve. Prototype: seqtools.Utilities::Int32 Merge(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Merge /in <fasta.DIR> [/out <out.fasta> /trim /unique /ext <*.fasta> /brief]

seqtools

This tools just merge the fasta sequence into one larger file. Prototype: seqtools.Utilities::Int32 SimpleMerge(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Merge.Simple /in <DIR> [/exts <default:*.fasta,*.fa> /line.break 120 /out <out.fasta>]

seqtools

Prototype: seqtools.Utilities::Int32 MirrorBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Mirror.Batch /nt <nt.fasta> [/out <out.csv> /mp /min <3> /max <20> /num_threads <-1>]

seqtools

Calculation in the multiple process mode?

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaFile Example:

[
    
]

Decalre: System.Boolean Example:

true

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:

{
    "Loci": "System.String",
    "MirrorSite": "System.String",
    "PalEnd": 0,
    "Palindrome": "System.String",
    "Start": 0
}

Prototype: seqtools.Utilities::Int32 FuzzyMirrors(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Mirror.Fuzzy /in <in.fasta> [/out <out.csv> /cut 0.6 /max-dist 6 /min 3 /max 20]

seqtools

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken Example:

{
    "Extension": {
        "DynamicHash": {
            "Properties": {
                
            },
            "source": [
                
            ]
        }
    },
    "SequenceData": "System.String",
    "Attributes": [
        "System.String"
    ]
}

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:

{
    "Loci": "System.String",
    "MirrorSite": "System.String",
    "PalEnd": 0,
    "Palindrome": "System.String",
    "Start": 0
}

Prototype: seqtools.Utilities::Int32 FuzzyMirrorsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Mirror.Fuzzy.Batch /in <in.fasta/DIR> [/out <out.DIR> /cut 0.6 /max-dist 6 /min 3 /max 20 /num_threads <-1>]

seqtools

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:

{
    "Loci": "System.String",
    "MirrorSite": "System.String",
    "PalEnd": 0,
    "Palindrome": "System.String",
    "Start": 0
}

Prototype: seqtools.Utilities::Int32 MirrorsVector(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Mirror.Vector /in <inDIR> /size <genome.size> [/out out.txt]

seqtools

This function will convert the mirror data to the simple segment object data Prototype: seqtools.Utilities::Int32 MirrorContext(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Mirrors.Context /in <mirrors.csv> /PTT <genome.ptt> [/trans /strand <+/-> /out <out.csv> /stranded /dist <500bp>]

seqtools

Enable this option will using genome_size minus loci location for the location correction, only works in reversed strand.

This function will convert the mirror data to the simple segment object data Prototype: seqtools.Utilities::Int32 MirrorContextBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Mirrors.Context.Batch /in <mirrors.csv.DIR> /PTT <genome.ptt.DIR> [/trans /strand <+/-> /out <out.csv> /stranded /dist <500bp> /num_threads -1]

seqtools

Enable this option will using genome_size minus loci location for the location correction, only works in reversed strand.

Prototype: seqtools.Utilities::Int32 MirrorGroups(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Mirrors.Group /in <mirrors.Csv> [/batch /fuzzy <-1> /out <out.DIR>]

seqtools

-1 means group sequence by string equals compared, and value of 0-1 means using string fuzzy compare.

Prototype: seqtools.Utilities::Int32 MirrorGroupsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Mirrors.Group.Batch /in <mirrors.DIR> [/fuzzy <-1> /out <out.DIR> /num_threads <-1>]

seqtools

Prototype: seqtools.Utilities::Int32 TrimNtMirrors(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Mirrors.Nt.Trim /in <mirrors.Csv> [/out <out.Csv>]

seqtools

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:

{
    "Loci": "System.String",
    "MirrorSite": "System.String",
    "PalEnd": 0,
    "Palindrome": "System.String",
    "Start": 0
}

RunNeedlemanWunsch Prototype: seqtools.Utilities::Int32 NW(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /nw /query <query.fasta> /subject <subject.fasta> [/out <out.txt>]

seqtools

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken Example:

{
    "Extension": {
        "DynamicHash": {
            "Properties": {
                
            },
            "source": [
                
            ]
        }
    },
    "SequenceData": "System.String",
    "Attributes": [
        "System.String"
    ]
}

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken Example:

{
    "Extension": {
        "DynamicHash": {
            "Properties": {
                
            },
            "source": [
                
            ]
        }
    },
    "SequenceData": "System.String",
    "Attributes": [
        "System.String"
    ]
}

Decalre: System.String Example:

"System.String"

Prototype: seqtools.Utilities::Int32 PalindromeBatchTask(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Palindrome.BatchTask /in <in.DIR> [/num_threads 4 /min 3 /max 20 /min-appears 2 /cutoff <0.6> /Palindrome /max-dist <1000 (bp)> /partitions <-1> /out <out.DIR>]

seqtools

Only search for Palindrome, not includes the repeats data.

Prototype: seqtools.Utilities::Int32 FilteringMatches(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Palindrome.Screen.MaxMatches /in <in.csv> /min <min.max-matches> [/out <out.csv>]

seqtools

Prototype: seqtools.Utilities::Int32 FilteringMatchesBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Palindrome.Screen.MaxMatches.Batch /in <inDIR> /min <min.max-matches> [/out <out.DIR> /num_threads <-1>]

seqtools

Prototype: seqtools.Utilities::Int32 PalindromeWorkflow(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Palindrome.Workflow /in <in.fasta> [/batch /min-appears 2 /min 3 /max 20 /cutoff <0.6> /max-dist <1000 (bp)> /Palindrome /partitions <-1> /out <out.DIR>]

seqtools

This is a single sequence fasta file.

Only search for Palindrome, not includes the repeats data.

Prototype: seqtools.Utilities::Int32 SelectByLocus(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Select.By_Locus /in <locus.txt> /fa <fasta/.inDIR> [/out <out.fasta>]

seqtools

Prototype: seqtools.Utilities::Int32 Sigma(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Sigma /in <in.fasta> [/out <out.Csv> /simple /round <-1>]

seqtools

Prototype: seqtools.Utilities::Int32 ConvertsAuto(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /SimpleSegment.AutoBuild /in <locis.csv> [/out <out.csv>]

seqtools

Decalre: Microsoft.VisualBasic.Data.csv.DocumentStream.File Example:

[
    
]

Decalre: SMRUCC.genomics.SequenceModel.NucleotideModels.SimpleSegment Example:

{
    "Complement": "System.String",
    "Ends": 0,
    "ID": "System.String",
    "SequenceData": "System.String",
    "Start": 0,
    "Strand": "System.String"
}

Prototype: seqtools.Utilities::Int32 ConvertMirrors(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /SimpleSegment.Mirrors /in <in.csv> [/out <out.csv>]

seqtools

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:

{
    "Loci": "System.String",
    "MirrorSite": "System.String",
    "PalEnd": 0,
    "Palindrome": "System.String",
    "Start": 0
}

Decalre: SMRUCC.genomics.SequenceModel.NucleotideModels.SimpleSegment Example:

{
    "Complement": "System.String",
    "Ends": 0,
    "ID": "System.String",
    "SequenceData": "System.String",
    "Start": 0,
    "Strand": "System.String"
}

Prototype: seqtools.Utilities::Int32 ConvertMirrorsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /SimpleSegment.Mirrors.Batch /in <in.DIR> [/out <out.DIR>]

seqtools

Prototype: seqtools.Utilities::Int32 SNP(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /SNP /in <nt.fasta> [/ref 0 /pure /monomorphic]

seqtools

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaFile Example:

[
    
]

Decalre: System.Int32 Example:

0

Decalre: System.Boolean Example:

true

Prototype: seqtools.Utilities::Int32 Split(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Split /in <in.fasta> [/n <4096> /out <outDIR>]

seqtools

Prototype: seqtools.Utilities::Int32 SubSet(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /subset /lstID <lstID.txt> /fa <source.fasta>

seqtools

Prototype: seqtools.Utilities::Int32 TimeDiffs(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Time.Diffs /in <aln.fasta> [/out <out.csv>]

seqtools

Convert the sequence data in a excel annotation file into a fasta sequence file. Prototype: seqtools.Utilities::Int32 ToFasta(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /To_Fasta /in <anno.csv> [/out <out.fasta> /attrs <gene;locus_tag;gi;location,...> /seq <Sequence>]

seqtools

Prototype: seqtools.Utilities::Int32 WriteSeeds(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools /Write.Seeds /out <out.dat> [/prot /max <20>]

seqtools

Polypeptide sequence 3 letters to 1 lettes sequence. Prototype: seqtools.Utilities::Int32 PolypeptideBriefs(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools -321 /in <sequence.txt> [/out <out.fasta>]

seqtools

Prototype: seqtools.Utilities::Int32 Align(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --align /query <query.fasta> /subject <subject.fasta> [/out <out.DIR> /cost <0.7>]

seqtools

Prototype: seqtools.Utilities::Int32 AlignSelf(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --align.Self /query <query.fasta> /out <out.DIR> [/cost 0.75]

seqtools

Prototype: seqtools.Utilities::Int32 Complement(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools -complement -i <input_fasta> [-o <output_fasta>]

seqtools

Prototype: seqtools.Utilities::Int32 DrawClustalW(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --Drawing.ClustalW /in <align.fasta> [/out <out.png> /dot.Size 10]

seqtools

Prototype: seqtools.Utilities::Int32 Hairpinks(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --Hairpinks /in <in.fasta> [/out <out.csv> /min <6> /max <7> /cutoff 3 /max-dist <35 (bp)>]

seqtools

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.ImperfectPalindrome Example:

{
    "Distance": 0,
    "Evolr": "System.String",
    "Left": 0,
    "Matches": "System.String",
    "MaxMatch": 0,
    "Palindrome": "System.String",
    "Paloci": 0,
    "Score": 0,
    "Site": "System.String"
}

Prototype: seqtools.Utilities::Int32 HairpinksBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --Hairpinks.batch.task /in <in.fasta> [/out <outDIR> /min <6> /max <7> /cutoff <0.6> /max-dist <35 (bp)> /num_threads <-1>]

seqtools

Prototype: seqtools.Utilities::Int32 BatchSearchImperfectsPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --ImperfectsPalindrome.batch.Task /in <in.fasta> /out <outDir> [/min <3> /max <20> /cutoff <0.6> /max-dist <1000 (bp)> /num_threads <-1>]

seqtools

Mirror Palindrome, search from a fasta file. Prototype: seqtools.Utilities::Int32 SearchMirrotFasta(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --Mirror.From.Fasta /nt <nt-sequence.fasta> [/out <out.csv> /min <3> /max <20>]

seqtools

This fasta file should contains only just one sequence.

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken Example:

{
    "Extension": {
        "DynamicHash": {
            "Properties": {
                
            },
            "source": [
                
            ]
        }
    },
    "SequenceData": "System.String",
    "Attributes": [
        "System.String"
    ]
}

Mirror Palindrome, and this function is for the debugging test Prototype: seqtools.Utilities::Int32 SearchMirrotNT(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --Mirror.From.NT /nt <nt-sequence> /out <out.csv> [/min <3> /max <20>]

seqtools

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:

{
    "Loci": "System.String",
    "MirrorSite": "System.String",
    "PalEnd": 0,
    "Palindrome": "System.String",
    "Start": 0
}

Prototype: seqtools.Utilities::Int32 BatchSearchPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --Palindrome.batch.Task /in <in.fasta> /out <outDir> [/min <3> /max <20> /num_threads <-1>]

seqtools

Prototype: seqtools.Utilities::Int32 SearchPalindromeFasta(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --Palindrome.From.Fasta /nt <nt-sequence.fasta> [/out <out.csv> /min <3> /max <20>]

seqtools

Fasta sequence file, and this file should just contains only one sequence.

Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken Example:

{
    "Extension": {
        "DynamicHash": {
            "Properties": {
                
            },
            "source": [
                
            ]
        }
    },
    "SequenceData": "System.String",
    "Attributes": [
        "System.String"
    ]
}

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:

{
    "Loci": "System.String",
    "MirrorSite": "System.String",
    "PalEnd": 0,
    "Palindrome": "System.String",
    "Start": 0
}

This function is just for debugger test, /nt parameter is the nucleotide sequence data as ATGCCCC Prototype: seqtools.Utilities::Int32 SearchPalindromeNT(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --Palindrome.From.NT /nt <nt-sequence> /out <out.csv> [/min <3> /max <20>]

seqtools

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:

{
    "Loci": "System.String",
    "MirrorSite": "System.String",
    "PalEnd": 0,
    "Palindrome": "System.String",
    "Start": 0
}

Prototype: seqtools.Utilities::Int32 ImperfectPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --Palindrome.Imperfects /in <in.fasta> [/out <out.csv> /min <3> /max <20> /cutoff <0.6> /max-dist <1000 (bp)> /partitions <-1>]

seqtools

Parsing the sequence segment from the sequence source using regular expression. Prototype: seqtools.Utilities::Int32 PatternSearchA(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools -pattern_search -i <file_name> -p <regex_pattern>[ -o <output_directory> -f <format:fsa/gbk>]

seqtools -pattern_search -i ~/xcc8004.txt -p TTA{3}N{1,2} -f fsa

The sequence input data source file, it can be a fasta or genbank file.

~/Desktop/xcc8004.txt

This switch specific the regular expression pattern for search the sequence segment, for more detail information about the regular expression please read the user manual.

N{1,5}TA

Optional, this switch value specific the output directory for the result data, default is user Desktop folder.

~/Documents/

Optional, specific the input file format for the sequence reader, default value is FASTA sequence file. fsa - The input sequence data file is a FASTA format file; gbk - The input sequence data file is a NCBI genbank flat file.

fsa

Prototype: seqtools.Utilities::Int32 FilterPerfectPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --PerfectPalindrome.Filtering /in <inDIR> [/min <8> /out <outDIR>]

seqtools

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.ImperfectPalindrome Example:

{
    "Distance": 0,
    "Evolr": "System.String",
    "Left": 0,
    "Matches": "System.String",
    "MaxMatch": 0,
    "Palindrome": "System.String",
    "Paloci": 0,
    "Score": 0,
    "Site": "System.String"
}

Prototype: seqtools.Utilities::Int32 RepeatsDensity(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools Repeats.Density /dir <dir> /size <size> /ref <refName> [/out <out.csv> /cutoff <default:=0>]

seqtools

Prototype: seqtools.Utilities::Int32 Reverse(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools -reverse -i <input_fasta> [-o <output_fasta>]

seqtools

Prototype: seqtools.Utilities::Int32 revRepeatsDensity(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools rev-Repeats.Density /dir <dir> /size <size> /ref <refName> [/out <out.csv> /cutoff <default:=0>]

seqtools

Batch search for repeats. Prototype: seqtools.Utilities::Int32 BatchSearch(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools Search.Batch /aln <alignment.fasta> [/min 3 /max 20 /min-rep 2 /out <./>]

seqtools

The input fasta file should be the output of the clustal multiple alignment fasta output.

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.RepeatsView Example:

{
    "Left": 0,
    "Locis": [
        0
    ],
    "SequenceData": "System.String"
}

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.RevRepeatsView Example:

{
    "Left": 0,
    "Locis": [
        0
    ],
    "SequenceData": "System.String",
    "RevLocis": [
        0
    ],
    "RevSegment": "System.String"
}

Prototype: seqtools.Utilities::Int32 GetSegment(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools -segment /fasta <Fasta_Token> [-loci <loci>] [/left <left> /length <length> /right <right> [/reverse]] [/ptt <ptt> /geneID <gene_id> /dist <distance> /downstream] -o <saved> [-line.break 100]

seqtools

Prototype: seqtools.Utilities::Int32 GetSegments(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --segments /regions <regions.csv> /fasta <nt.fasta> [/complement /reversed /brief-dump]

seqtools

If the sequence is on the complement strand, reversed it after complement operation?

If this Boolean switch is set on, then all of the reversed strand segment will be complemenet and reversed.

If this parameter is set up true, then only the locus_tag of the ORF gene will be dump to the fasta sequence.

Prototype: seqtools.Utilities::Int32 ToVector(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --ToVector /in <in.DIR> /min <4> /max <8> /out <out.txt> /size <genome.size>

seqtools

Translates the ORF gene as protein sequence. If any error was output from the console, please using > operator dump the output to a log file for the analysis. Prototype: seqtools.Utilities::Int32 Translates(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --translates /orf <orf.fasta> [/transl_table 1 /force]

seqtools

ORF gene nt sequence should be completely complement and reversed as forwards strand if it is complement strand.

This force parameter will force the translation program ignore of the stop code and continute sequence translation.

Available index value was described at http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#SG25

Prototype: seqtools.Utilities::Int32 Trim(Microsoft.VisualBasic.CommandLine.CommandLine)

seqtools --Trim /in <in.fasta> [/case <u/l> /break <-1/int> /out <out.fasta> /brief]

seqtools

Adjust the letter case of your sequence, l for lower case and u for upper case. Default value is upper case.

Adjust the sequence break when this program write the fasta sequence, default is -1 which means no break, write all sequence in one line.