Fasta converter

Author: d | 2025-04-24

GBK to FASTA converter : GenBank to FASTA is a freeware program will convert GenBank (gbk) file format to FASTA format. ABI to FASTA converter: ABI to FASTA Converter is a free tool FASTA to multi-Fasta format converter. Program merges FASTA files into a single multi-FASTA. Sample file format converter/merger. SCF, ABI, SEQ, FASTA. Convert your Fasta files in seconds! FASTA to multiFASTA format converter. This program will merge all FASTA protein files in a folder into a single multi-FASTA

FASTA to FASTA (Online Free)Convert FASTA to FASTA

Seq Format Converter is an easy-to-use application that gives you the possibility to convert files with nucleotide or peptide sequences to tab-delimited CSV and Fasta (biological sequence) format.It doesn't have advanced output customization settings, making it ideal for all users who want to carry out tasks quickly, without having to worry about complicated features.Setup, requirements, and interfaceInstalling it is a speedy job that shouldn't give you any trouble. Before running the setup kit, however, you should download and install .NET Framework unless you already have it, otherwise it won't work.Easily convert files to CSV or Fasta formatSeq Format Converter has a clean and intuitive interface. This is represented by just one window that contains a large area for dropping files while exploring disk directories, along with three buttons for converting the items to Fasta and CSV format, as well as for modifying the default output directory (for both types of extensions).Worth noting is that batch processing isn't supported. You can convert only one file at a time. This might be inconvenient for users looking to handle bigger tasks as fast as possible, since they are forced to manage one file at a time.Lightweight and straightforward file converterThe software program worked well in our evaluation, without triggering the operating system to hang, crash or prompt errors. It didn't use a lot of computer resources, since it needed low CPU and RAM to perform conversions.On the other hand, Seq Format Converter lacks richer options and customization settings to meet the requirements of experienced users. For instance, it doesn't give you the possibility to preview output files, nor to convert multiple items at the same time. We are also taking note of the fact that that it hasn't been updated for a while.Filed underSequence conversion FASTA converter FASTAQ conversion Nucleotide Sequence Peptide Converter

FASTA to FASTA (Online Free) Convert FASTA to FASTA - Docpose

Comprendiendo los formatos de archivo FASTA y FAEl formato FASTA es un formato basado en texto para representar secuencias de nucleótidos o secuencias de péptidos. Cada secuencia en un archivo FASTA comienza con una descripción en una sola línea, seguida por líneas de datos de la secuencia. La línea de descripción se distingue de los datos de la secuencia por un símbolo de mayor que (>) al principio.El formato de archivo FA es esencialmente el mismo que el formato FASTA. La diferencia radica principalmente en la extensión del archivo utilizada. Ambos formatos se usan indistintamente en bioinformática para el almacenamiento de datos de secuencias.Convertir FASTA a FAConvertir un archivo FASTA a un archivo FA es sencillo ya que implica cambiar la extensión del archivo. Esto se puede hacer manualmente o utilizando un script simple.Mejor software para la conversión de FASTA a FAAunque muchas herramientas de bioinformática pueden manejar tanto archivos FASTA como FA, aquí hay algunos métodos para realizar la conversión:Usando la línea de comandosPuede usar la línea de comandos para renombrar la extensión del archivo:mv filename.fasta filename.faEste comando renombrará el archivo de filename.fasta a filename.fa.Usando un editor de textoAbra el archivo FASTA en un editor de texto y guárdelo con la extensión .fa. Por ejemplo, en Notepad++: Abra el archivo FASTA. Haga clic en File → Save As. Cambie la extensión del archivo a .fa y guarde.Usando software de bioinformáticaSoftware como BioEdit o Geneious puede abrir archivos FASTA y guardarlos con una extensión diferente: Abra el archivo FASTA en el software. Use la opción File → Export para guardar el archivo con una extensión .fa. Nota: Este registro de conversión de fasta a fa está incompleto, debe verificarse y puede contener imprecisiones. Por favor, vote a continuación si esta información le resultó útil o no.

bio fasta: convert to FASTA

3.2 Data input formats Geneious Prime version 2022.1 can import the following file formats: Format Extensions Data types Common sources BED *.bed Annotations UCSC Common Assembly Format *.caf Contigs Sequencher Clone Manager molecule *.cm5 Sequences and annotations Clone Manager Clustal *.aln Alignments ClustalX CSFASTA *.csfasta Color space FASTA ABI SOLiD Comma/Tab Separated Values *.csv, *.tsv Spreadsheet files Microsoft Excel DNAStar *.seq, *.pro Nucleotide & protein sequences DNAStar DNA Strider *.str Sequences DNA Strider (Mac program), ApE Embl/UniProt *.embl, *.swp Sequences Embl, UniProt EMBOSS codon usage table *.cusp, *.cut Codon usage table EMBOSS cusp tool Endnote (8.0 or 9.0) XML *.xml Journal article references Endnote, Journal article websites Excel spreadsheet *.xlsx, *.xls Spreadsheet files Microsoft Excel FASTA *.fasta, *.fas, *fasta.gz etc. Sequences, alignments PAUP*, ClustalX, BLAST, FASTA FASTQ *.fastq, *.fq, *fastq.gz etc. Sequences with quality Illumina and other NGS sequencers GCG *.seq Sequences GCG GCG codon usage table *.cod Codon usage table GCG CodonFrequency tool, GenBank *.gb, *.xml Nucleotide & protein sequences GenBank Geneious *.xml, *.geneious Preferences, databases Geneious Geneious Education *.tutorial.zip Tutorial, assignment etc. Geneious GFF, GFF3, GTF *.gff, *.gff3, *.gtf Annotations NCBI, Ensembl and other genome browsers MEGA *.meg Alignments MEGA Molecular structure *.pdb, *.mol, *.xyz, *.cml, *.gpr, *.hin, *.nwo 3D molecular structures 3D structure databases and programs Newick *.tre, *.tree, etc. Phylogenetic trees PHYLIP, Tree-Puzzle, PAUP*, ClustalX Nexus *.nxs, *.nex Trees, Alignments PAUP*, Mesquite, MrBayes & MacClade PDB *.pdb 3D Protein structures SP3, SP2, SPARKS, Protein Data Bank PDF *.pdf Documents, presentations Adobe Writer, LATEX, Miktex Phrap ACE *.ace Contig assemblies Phrap/Consed PileUp *.msf Alignments pileup (gcg) PIR/NBRF *.pir Sequences, alignments NBRF PIR Qual *.qual Quality file Associated with a FASTA file Raw sequence text *.seq Sequences Any file that contains only a sequence Rich Sequence Format *.rsf Sequences, alignments GCGs NetFetch SAM/BAM *.sam, *.bam Contigs SAMtools Sequence Chromatograms *.ab1, *.scf Raw sequencing trace & sequence Sequencing machines SnapGene sequence *.dna, *prot Sequences and annotations SnapGene Text/html .txt, .rtf, .html Any text Simple text editors VCF *.VCF Annotations 1000 Genomes Project Vector NTI sequence *.gb, *.gp Nucleotide & protein sequences Vector NTI Vector NTI/AlignX alignment *.apr Alignments Vector. GBK to FASTA converter : GenBank to FASTA is a freeware program will convert GenBank (gbk) file format to FASTA format. ABI to FASTA converter: ABI to FASTA Converter is a free tool FASTA to multi-Fasta format converter. Program merges FASTA files into a single multi-FASTA. Sample file format converter/merger. SCF, ABI, SEQ, FASTA. Convert your Fasta files in seconds! FASTA to multiFASTA format converter. This program will merge all FASTA protein files in a folder into a single multi-FASTA

Free multi-fasta to fasta converter Download - multi-fasta to fasta

Genes in the nucleic fasta file (-fn) must be the same than the ID of the proteins in the protein fasta file (-fp) and in the annotation file (-a).emapper2gbk genomesFor each genomes, inputs are:a nucleotide fasta file containing the sequence of each contigs/chromosomes for the genome or a folder containing multiple nucleotide fasta files.the proteome corresponding to the genome or a folder containing the corresponding protein sequences to the nucleotide sequences (having the same name as the nucleotides files).the GFF file corresponding to the genome or a folder containing multiple GFF files (each GFF files must have the same name as the corresponding nucleotide files).the annotation file obtained after Eggnog-mapper annotation (usually xxx.emapper.annotation) or a folder with multiple annotation files (must be the same name as nucleotide fasta file and ends with '.tsv' extension)In addition, as optional files:the name of the considered organism (can be "bacteria"), a full lineage of the organism (such as Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia,Escherichia coli) or a file with organisms names (matching the genomes names).the number of available cores for multiprocessing (when working on multiple genomes).a go-basic file of GO ontology (if not given, emapper2gbk will download a copy and use it).Example:Input with files:nucleotide_sequences.fnaprotein_sequence.faaannotation.emapper.annotationgenome.gffInput with folders:nucleotide_sequences├── genome_1.fna├── genome_2.fnaprotein_sequence├── genome_1.faa├── genome_2.faaannotation├── genome_1.tsv├── genome_2.tsvgff├── genome_1.gff├── genome_2.gffThe ID in the chromosome/contigs/scaffolds fasta file (-fn) must correspond to region in the gff file (-g).Then the genes in the region will be found and the child CDS associated to the genes wil be extracted.The CDS ID must be the same than the ID in the protein fasta file (-fp) and the ID in the eggnog-mapper annotation file (-a).By default emapper2gbk searches for inheritance between genes and CDS in the GFF files.A gene feature is required and the CDS feature must have the gene feature as a parent, like in this example:##gff fileregion_1 RefSeq region

cfe-lab/fasta-converter: Converts FASTA to CSV and CSV to FASTA

Similar to formulating a series of bullet points in natural language. Based on experience of a number of colleagues who have had zero prior programming experience, it takes between a day and a week to master R to a level which allows to confidently work with proteomics data (you only need very basics). Indeed, it may take one an hour or so to make several plots in Excel, and only several minutes in R. But most importantly, if you need to adjust your plots or the underlying data, it may be again just minutes in R (change a couple of lines of code and re-run the script), overall it greatly simplifies any kind of work with proteomics data and eventually saves a lot of time. We recommend starting here This particular section nicely demonstrates how easy it is to create informative diagrams in R with just one or two lines of code.GUI settings reference InputConvert to .dia Convert the selected raw files to DIA-NN's .dia format, for faster subsequent processing, and save them either to the same folder as the respective source raw files or to Temp/.dia dir (Output pane), if the latter is specified. Conversion is recommended for Sciex files, typically makes little difference for Thermo files and is not recommended for Bruker files.Spectral library specify the spectral library.Add FASTA add one or more FASTA files. FASTA files must always be specified if Protein inference is not disabled (see below) or you would like to obtain protein-matched phosphosite information. The only reason not to specify FASTA files is a situation when you are using an empirical library generated with the use of a different FASTA database that is not available, and in such case specifying FASTA files will overwrite the annotation of protein sequence IDs in the library, potentially

Convert your Fasta files in seconds! FASTA to multi-FASTA

Emapper2gbk: creation of genbank files from Eggnog-mapper annotation outputsStarting from fasta and Eggnog-mapper annotation files, build a gbk file that is suitable for metabolic network reconstruction with Pathway Tools. Adds the GO terms and EC numbers annotations in the genbank file.There are two main modes:genes mode: suitable when a list of isolated genes/proteins have been annotated with Eggnog-mapper, typically the gene catalogue of a metagenome.genomes mode: usually when focusing on a single organism, with a .gff file. The creation of genbanks can be performed in parallel by providing directories (with matching names for genomes, proteomes and annotation files) as inputs.If you use emapper2gbk, please citeBelcour* A, Frioux* C, Aite M, Bretaudeau A, Hildebrand F, Siegel A. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. eLife 2020;9:e61968 .Table of contentsMain inputsemapper2gbk genesemapper2gbk genomesTaxonomic informationDependencies and installationDependenciesInstallUsageLicenseMain inputsemapper2gbk genesFor each annotated list of genes, inputs are:a nucleotide fasta file containing the CDS sequence of each genes or a folder containing multiple nucleotide fasta files.the translated sequences in amino-acids in fasta or a folder containing the corresponding protein sequences to the nucleotide sequences (must be the same name).the annotation file obtained after Eggnog-mapper annotation (usually xxx.emapper.annotation) or a folder with multiple annotation files (must be the same name as nucleotide fasta file and ends with '.tsv' extension).In addition, as optional files:the name of the considered organism (can be "bacteria" or "metagenome"), a full lineage of the organism (such as Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia,Escherichia coli) or a file with organisms names (matching the genomes names).the merge option to merge genes into fake contigs.the number of available cores for multiprocessing (when working on multiple genomes).a go-basic file of GO ontology (if not given, emapper2gbk will download a copy and use it).Example:Input with files:nucleotide_sequences.fnaprotein_sequence.faaannotation.emapper.annotationInput with folders:nucleotide_sequences├── gene_list_1.fna├── gene_list_2.fnaprotein_sequence├── gene_list_1.faa├── gene_list_2.faaannotation├── gene_list_1.tsv├── gene_list_2.tsvTo work the ID of the

FASTA Converter - Convert FASTA Online Free - Docpose

During mutation during decoy generation to be at least X in absolute value, default 15.0--dg-max-mut [X] aim for the precursor mass shift during mutation during decoy generation not to exceed X in absolute value, default 50.0--dir [folder] specifies a folder containing raw files to be processed. All files in the folder must be in .raw, .wiff, .mzML or .dia format--dir-all [folder] as --dir, but recursive over subfolders--direct-quant disable QuantUMS and use legacy DIA-NN quantification algorithms instead, also disables channel-specific protein quantification when analysing multiplexed samples--dl-no-fr when using the deep learning predictor, prediction of fragment intensities will not be performed--dl-no-im when using the deep learning predictor, prediction of ion mobilities will not be performed--dl-no-rt when using the deep learning predictor, prediction of retention times will not be performed--duplicate-proteins instructs DIA-NN not to skip entries in the sequence database with duplicate IDs (while by default if several entries have the same protein ID, all but the first entry will be skipped)--export-quant add fragment quantities, fragment IDs and quality information to the .parquet output report--ext [string] adds a string to the end of each file name (specified with --f)--f [file name] specifies a run to be analysed, use multiple --f commands to specify multiple runs--fasta [file name] specifies a sequence database in FASTA format (full support for UniProt proteomes), use multiple --fasta commands to specify multiple databases--fasta-filter [file name] only consider peptides matching the stripped sequences specified in the text file provided (one sequence per line), when processing a sequence database--fasta-search instructs DIA-NN to perform an in silico digest of the sequence database--fixed-mod [name],[mass],[sites],[optional: 'label'] - adds the modification name to the list of recognised names and specifies the modification as fixed. Same syntax as for --var-mod. Has an effect of (i) applying fixed modifications during FASTA digest or (ii) declaring fixed modifications. GBK to FASTA converter : GenBank to FASTA is a freeware program will convert GenBank (gbk) file format to FASTA format. ABI to FASTA converter: ABI to FASTA Converter is a free tool FASTA to multi-Fasta format converter. Program merges FASTA files into a single multi-FASTA. Sample file format converter/merger. SCF, ABI, SEQ, FASTA. Convert your Fasta files in seconds! FASTA to multiFASTA format converter. This program will merge all FASTA protein files in a folder into a single multi-FASTA

FASTA Converter - Convert fasta Online Free - Docpose

Replacing protein names, genes and descriptions.Reannotate option allows to reannotate the spectral library with protein information from the FASTA database, using the specified digest specificity.Contaminants Adds common contaminants from the Cambridge Centre for Proteomics (CCP) database and automatically excludes them from quantification, see the description of the --cont-quant-exclude option. This option applies when generating a predicted spectral library from a FASTA database or analysing using such a library, if it was generated with Contaminants enabled. Precursor ion generationFASTA digest instructs DIA-NN to in silico digest the sequence database and apply specified modifications (see below), to generate a predicted spectral library in silico. This option must be unchecked when analysing raw data.Deep learning-based spectra, RTs and IMs prediction instructs DIA-NN to perform deep learning-based prediction of spectra, retention times and ion mobility values. This allows not only to make in silico spectral libraries from sequence databases, but also to replace spectra/RTs/IMs in existing libraries with predicted values. This option must not be used together with raw data analysis, i.e. in silico predicted library generation must be done in a separate step.Protease use pre-configured digest specificity, can be customised using the --cut command. Only affects FASTA digest or reannotation.Missed cleavages set the maximum number of missed cleavages allowed. Only affects FASTA digest. Increases the search space and hence the analysis time, setting to 1 is almost always the best, in some cases 2 may be beneficial, higher values are likely detrimental.Maximum number of variable modifications sets the maximum total number of occupied variable modification sites per peptide, only affects FASTA digest. Reasonable values are usually in 1 to 3 range, setting to 4 or higher is almost always detrimental. Substantially increases the search space and hence the analysis time and RAM usage, may have some detrimental effects on the identification numbers if

FASTA Converter - Convert fasta Online Free - FileProInfo

Multiple mode, "bacteria" as default nameemapper2gbk genes -fn genome_dir/ -fp proteome_dir/ -n metagenome -o gbk_dir/ -a eggnog_annotation_dir/ [-go go-basic.obo]* Genomic - multiple mode, tsv file for organism namesemapper2gbk genes -fn genome_dir/ -fp proteome_dir/ -nf matching_genome_orgnames.tsv -o gbk_dir/ -a eggnog_annotation_dir/ [-go go-basic.obo]* Metagenomicemapper2gbk genes -fn genome_dir/ -fp proteome_dir/ -o gbk_dir/ -a gene_cat_ggnog_annotation.tsv --one-annot-file [-go go-basic.obo]You can give the GO ontology as an input to the program, it will be otherwise downloaded during the run. You can download it here: .The program requests the NCBI database to retrieve taxonomic information of the organism. However, if the organism is "bacteria" or "metagenome", the taxonomic information will not have to be retrieved online.Hence, if you need to run the program from a cluster with no internet access, it is possible for a "bacteria" or "metagenome" organism, and by providing the GO-basic.obo file.For specific help on each subcommand use: emapper2gbk {cmd} --helpoptional arguments:-h, --help show this help message and exit-v, --version show program's version number and exitsubcommands:valid subcommands:{genes,genomes} genes genes mode : 1-n annot, 1-n faa, 1-n fna (gene sequences) --> 1 gbk genomes genomes mode: 1-n contig/chromosome fasta, 1-n protein fasta, 1-n GFF, 1-n annot --> 1 gbk">usage: emapper2gbk [-h] [-v] {genes,genomes} ...Starting from fasta and Eggnog-mapper annotation files, build a gbk file that is suitable for metabolic network reconstruction with Pathway Tools. Adds the GO terms and EC numbers annotations in the genbank file.Two modes:- genomes (one genome/proteome/gff/annot file --> one gbk).- genes with the annotation of the full gene catalogue and fasta files (nucleic and protein) corresponding to list of genes.Examples:* Genomic - single modeemapper2gbk genomes -fn genome.fna -fp proteome.faa -gff genome.gff -n "Escherichia coli" -o coli.gbk -a eggnog_annotation.tsv [-go go-basic.obo]* Genomic - multiple mode, "bacteria" as default nameemapper2gbk genes -fn genome_dir/ -fp proteome_dir/ -n metagenome -o gbk_dir/ -a eggnog_annotation_dir/ [-go go-basic.obo]*. GBK to FASTA converter : GenBank to FASTA is a freeware program will convert GenBank (gbk) file format to FASTA format. ABI to FASTA converter: ABI to FASTA Converter is a free tool

Fasta to Fasta Converter, choose file and convert it now - Bugaco

With all of the options available.Building a map with FASTA sequenceThis is the recommended use case, when you have access to a medium-high resolution cryo-EM map (resolutions exceeding 4 Å) as well as a FASTA files with all of your protein, RNA, and DNA sequences.Let's say the map's name is map.mrc and the (protein) sequence file is prot.fasta. To build your model in a directory named output, you run:model_angelo build -v map.mrc -pf prot.fasta -o outputIf you would like to build nucleotides as well, you need to provide the RNA and DNA portions of your sequences in different files like somodel_angelo build -v map.mrc -pf prot.fasta -df dna.fasta -rf rna.fasta -o outputIf you only have RNA or DNA, you can drop the other input.If the output of the program halts before the completion of GNN model refinement, round 3 / 3, there was a bug that you can see in output/model_angelo.log. Otherwise, you can find your model in output/output.cif. The name of the mmCIF file is based on the output folder name, so if you specify, for example, -o testing/test/model_building, the model will be in testing/test/model_building/model_building.cif.Building a map with no FASTA sequenceIf you have a sample where you do not know all of the protein sequences that occur in the map, you can run model_angelo build_no_seq instead.This version of the program uses a network that was not trained with input sequences, nor does it do post-processing on the built map.Instead, in addition to a built model, it provides you with HMM profile files that you can use to search a database such as UniRef with HHblits.You run this command:model_angelo build_no_seq -v map.mrc -o outputThe model will be in output/output.cif as before.Using the HMM search procedureIf you have a map and would like to identify new proteins, first build it with the no sequence option as above.You will have the model as an mmCIF.Now there are also HMM profiles for each chain in HMMER3 format here: output/hmm_profiles.To do a sequence search, you should first download a fasta file that includes your proteins of interest. Often, this will be the proteome of