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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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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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Install BioPython Run following script: from Bio import SeqIO records = SeqIO.parse ("THIS_IS_YOUR_INPUT_FILE.stockholm", "stockholm") count = SeqIO.write (records, "THIS_IS_YOUR_OUTPUT_FILE.fasta", "fasta") print ("Converted %i records" % count) Or you can use this site as online stockholm to fasta converter by selecting your formats & file.
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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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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. 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(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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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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Convert from: to: Alphabet: None DNA RNA Protein Nucleotide To learn more on how to convert files on your desktop, pick pair of formats above and follow updated link. Supported formats are: clustal embl fasta fastq genbank nexus phylip seqxml stockholm tab xdna and many others. Using BioPython backend for conversions.
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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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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
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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
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