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converts an existing file a.fasta from FASTA to Stockholm format.. $ seqmagick convert --head 5 examples/test.fasta examples/test.head.fasta $ seqmagick info examples/test*.fasta name alignment min_len max_len avg_len num_seqs examples/test.fasta FALSE 972 9719 1573.67 15 examples/test.head.fasta FALSE 978 990 984.00 5
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EMBL-EBI. EMBOSS seqret reads and writes (returns) sequences. It is useful for a variety of tasks, including extracting sequences from databases, displaying sequences, reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions.
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1. Input the format of the input file: 2. Select a output file format: Upload file（no exceeds 10MB） Supported file formats by this tool abi: Reads the ABI "Sanger" capillary sequence traces files, including the PHRED quality scores for the base calls. This allows ABI to FASTQ conversion.
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fasta_to_stockholm: Converts FASTA to STOCKHOLM Description The HMMER binary version for windows does not recognize FASTA files to build the This function creates a STOCKHOLM file readable by HMMER 3.0 Usage fasta_to_stockholm(fasta.file) Arguments fasta.file FASTA object to be converted Value TRUE/FALSE Powered byDataCamp
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if I understood the Stockholm format correct it is an alignment format. So to convert fasta to it, it is neccessary that the fasta sequence contains alignment characters to mark gaps between the aligned sequences. That said all sequences must have the same length. The converter is not intended to do the alignment. Seems like an XY problem.
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Fasta
fasta_to_stockholm(fasta.file)} \ arguments {\ item {fasta.file}{FASTA object to be converted}} \ value {TRUE / FALSE} \ description {The HMMER binary version for windows does not recognize FASTA files to build the: hmm profile. This function creates a STOCKHOLM file readable by HMMER 3.0} \ keyword {internal} Copy lines
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Hello I've multiple sequences in stockholm format, at the top of every alignment there is a accession ID, for ex: '#=GF AC PF00406' and '//' --> this is the end of the alignment.When I'm converting the stockholm format to fasta format I need PF00406 in the header of every sequence of the particular alignment. Some times there will be multiple stockholm alignments in one file.
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1 fasta_to_stockholm (fasta.file) Arguments Value TRUE/FALSE effectR documentation built on May 1, 2019, 7:28 p.m. Related to. The HMMER binary version for windows does not recognize FASTA files to build the hmm profile. This function creates a STOCKHOLM file readable by HMMER 3.0
Brygga Stockholm Skärgård Värmdö. Red Mount AB. +46700534688 AB Sjöliv
Description The HMMER binary version for windows does not recognize FASTA files to build the hmm profile. This function creates a STOCKHOLM file readable by HMMER 3.0 Usage 1 fasta_to_stockholm (fasta.file) Arguments fasta.file FASTA object to be converted Value TRUE/FALSE
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Converts FASTA to STOCKHOLM Description The HMMER binary version for windows does not recognize FASTA files to build the hmm profile. This function creates a STOCKHOLM file readable by HMMER 3.0 Usage fasta_to_stockholm (fasta.file) Arguments fasta.file FASTA object to be converted Value TRUE/FALSE
Detaljer « Saxarens Brygg AB i Stockholm Fasta bryggor, flytbryggor
Fasta to Stockholm Sequence Converter Convert file from: to Alphabet: None DNA RNA Protein Nucleotide Input format: fasta This refers to the input FASTA file format introduced for Bill Pearson's FASTA tool, where each record starts with a '>' line. Resulting sequences have a generic alphabet by default.
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Project description seqconverter The command-line program seqconverter can read and write text files containing aligned or unaligned DNA or protein sequences. The program understands most standard and some non-standard formats (fasta, Nexus, Phylip, Clustal, Stockholm, tab, raw, Genbank, How).
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