Sequence format conversion
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[edit] Sequence format conversion - Quick Links
[edit] Sequence format conversion - Web Resources Descriptions in Detail
Chromatogram Explorer- Automatically exploring, converting and trimming chromatograms
Chromatogram Explorer is a very easy to use tool that will list all chromatogram files (SCF, ABI, AB1, AB) in the current folder. You can view the chromatograms while browsing through folders using its integrated Windows Explorer. Chromatogram Explorer can also trim low quality bases at the ends of your samples with a single push of a button! Now you can process/sort/search chromatograms in seconds.
How to use it
Start Chromatogram Explorer, and locate the folder that contains your chromatogram files. All chromatogram files (ABI/SCF) will be shown in the right panel. Low quality ends (that will be trimmed) are shown in dark red. Press 'Save' and your file will be saved as SCF of FASTA (you can choose the output format), while the low quality bases at the ends will be trimmed. Chromatogram Explorer is so small that you can put it on a floppy disk of Flash stick and taken it with you.
ABI to FASTA converter
This free tool will batch convert all (selected) ABI files to FASTA files. All you need to do is to locate your ABI chromatogram files and press the CONVERT button. It offers a great relief for the biologists who must convert hundreds of ABI chromatogram files manually. With our automatic ABI to FASTA converter you can convert hundreds or thousands of ABI chromatogram files in seconds. All with A SINGLE PUSH OF A BUTTON!
Install process: You do not need to install it or unpack it. Just download the program and double click to run it. ABI to FASTA converter does not need additional software, updates, DLL's or Java to run. To uninstall it, just delete the program.
FASTA to multi-FASTA converter
This freeware tool will look for all FASTA files in the specified folder and will merge their content in a single file, generating a standard or custom Multi-FASTA file. The size of the program is only 0.7MB. No Java or additional modules are required to be installed.
Multi-FASTA to FASTA converter
This freeware program will split a multi-FASTA file in multiple standard FASTA files. The size of the program is only 0.6MB
DNA Baser [Free converter tool]
Easy to use software package providing batch DNA sequence assembly, contig editing, chromatogram viewer and rapid detection of mutations in DNA sequences. Files supported by DNA Baser are any type of ABI (ABI, AB, AB1), SCF, FASTA, SEQ.
It has a fast assembly engine with a range of features that greatly speeds the process of sequence assembly and mutation analysis. DNA Baser is the only software which allow batch assembly (it automatically scan a folder for samples that belongs to the same contig, based on a name pattern, and assemble those samples without users intervention). It can also 'assemble to reference'. The program is fully functional for 60 days but the format conversion module is working even after the 60 days threshold.
The size of the program is 2MB.
ReadSeq
Sequence format converstion: converts input DNA/AA sequence to specified format. Input format is determined automatically.. Automatically detects input format and converts into FASTA, Stanford, Genbank, NBRF, EMBL, GCG, DNAStrider, Fitch, Phylip, raw, PIR, MSF or NEXUS sequence formats.
The Scriptome - Protocols for Manipulating Biological Data. The Scriptome is a set of easy to use tools that filter, format, and merge data in tabular or common biological formats, and you don't have to be a programmer to use them. Use single tools to take a quick look at data, or string tools together in a protocol to explore the data more deeply. Good for *nix, Mac or Windows users.
SeqVerter by GeneStudio, Inc. (free)
Converts sequence between different formats (Windows 2000/XP). Reads the following input: ABI traces (*.abi and *.ab1), CLUSTAL, DCSE, DNASIS, DNAStar (LaserGene), DNAStrider (including binary), EMBL, FASTA, GDE, GenBank, IBI/Pustell, Macaw, MSF, Nexus/PAUP, PHYLIP Interleaved, PIR/NBRF, SCF 2.0 and SCF 3.0 traces, Swiss-Prot, and TreeCon. Writes the following output formats: CLUSTAL, DNASIS, DNAStar (LaserGene), FASTA, FASTA (Strict), and FASTA (SequIn), GenBank, IBI/Pustell, MSF, Nexus/PAUP, PHYLIP Interleaved, and TreeCon. Full export and import compatibility with Mac, PC, and UNIX text file formats.
ClustalW_Convert
Alignment format conversion between many formats. ClustalW_Convert converts from EMBL/Swiss-Prot, NBRF/PIR, FASTA (Pearson), Clustal (*.aln), GCG/MSF (pileup), GDE formats to GCG/MSF, ClustalW, NBRF/PIR, GDE and Phylip formats.
| DPL Forum: Too few categories! |
ABI View
Reads ABI file and display the trace (EMBOSS) and converts trace files into fasta format. ABIView is primarily a sequencing trace viewing program which also converts ABI (commonly suffixed *.abi and *.ab1) sequence trace files derived from automatic dna sequencing into FASTA (Pearson) format.
DNA String Utilities
Simple web-based sequence manipulation including reverse comlement, translation, and a nice cleanup function which removes numbers and whitespace from an input field, for example raw sequence cut from a GenBank record.
ReadSeq (java)
Biosequence inter-conversion tool. Guesses what your input sequence data format is, and converts it to what your software knows how to handle.Version (2001) of ReadSeq which converts sequences to FASTA, XML, AceDB, EMBL, GCG, Stanford, Clustal, Pretty, Nexus, NBRF, DNAStrider, Phylip, MSF, FlatFeat, GFF, gb Genbank, PIR and IG Stanford formats. Written in Java.
DNA Duster
Removes formatting characters and other non-sequence related stuff from a sequence. It outputs in a variety of formats including as translated protein.
sreFormat
HMMER tool to convert sequence file to different format. Converts sequence to FASTA, EMBL, GenBank, GCG, MacStrider, Zuker mfold, Intelligenetics, St Louis, PIR, Pfam, GCG, Phylip, Selex formats.
FmtSEQ
Format Sequence converts sequences between 22 sequence format types. FMTSEQ converts sequences between many formats including among others raw, plain, EMBL, Swiss-prot, GenBank, PIR, NBRF, GCG, ASN, MRF, Phylip, Pretty and ClustalW formats.
MView
Multiple alignment viewer and format converter. Converts multiple alignments from FASTA, MSF, Phylip, MaxHom (HSSP), plain, MULTAL or MULTAS, MIPS-ALN to HTML, GCG, FASTA, PIR, or RDB relational database formatted table form. Includes residue coloring facility.
Squizz
Sequence or alignment format convertor and checker. Allows the verification of sequence or sequence alignment formats and conversion into the following formats: Clustal, EMBL, Fasta, GCG, Intelligenetics, GDE, GenBank, NBRF, MSF, Nexus, Phylip, PIR Codata, Raw and SwissProt.
Protein Duster
Removes formatting characters and other non-sequence related stuff from a protein sequence.
GenBank2XML
Genbank to XML conversion tool. Converts GenBank formatted sequence to XML. Input sequence can be pasted, uploaded or fetched using SRS and its accession number.
PrettySeq
Sequence format conversion tool still under development (2006-7) allowing nucleic acid sequence to be numbered and converted into specified wordsizes, and numbers of columns and rows, as well as complement and reversed.
