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This function creates a STOCKHOLM file readable by HMMER 3.0","}","\\keyword {internal}"],"stylingDirectives":null,"csv":null,"csvError":null,"dependabotInfo": {"showConfigurationBanner":false,"configFilePath":null,"networkDependabotPath":"/grunwaldlab/effectR/network/updates","dismissConfigurationNoticePath":"/settings/dismiss-notice/dependabot.
Fasta
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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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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1. 选择输入文件的格式: fasta 2. 选择输出文件的格式: stockholm 上传文件（不超过10MB） 文件格式转换工具支持的格式 abi: 读取ABI "Sanger" 毛细管测序文件, 包括对碱基判定的PHRED质量得分，因此可以执行ABI 到 FASTQ 的格式转换. abi-trim: 和"abi"一样，但是是经过Mott算法修剪过的序列. ace: ace格式拼接结果文件 cif-atom: 根据原子坐标确定结构中出现的（部分）蛋白质序列 cif-seqres: 读取大分子晶体信息文件 (mmCIF)，确定蛋白质的完整序列 clustal: Clustal X 和 Clustal W软件的比对结果. embl: EMBL平面文件格式
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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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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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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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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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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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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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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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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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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).