Best Sequence File Format Conversion Tools

Previously we have discussed about different file formats and their importance in today's research scenario especially in bioinformatics research. No doubt there are tons of tools there and so obviously there are plethora of file format also. Since a single program can't perform every task and a single file format can't be accepted by all bioinformatics software. Therefore, you can get several bioinformatics resources, both servers and softwares, that are ready to convert sequence file format  for free. here we are giving the link of 5 major and best (atleast in my opinion :) ) to change the sequence file format. These server generally have following functionality : 


  • Complement - Create the complement DNA or RNA strand.
  • Inverse - Create the inverse of given sequences
  • T to U - Replace all thymidine by uracil.
  • U to T - Replace all uracil by thymidine. 
  • UCase - Convert the sequence into upper case. 
  • LCase - Convert the sequence into lower case. 


1. Readseq -biosequence conversion tool : One of the most popular server to change the sequence file format. During conversion you can choose the output format (1), sequence case (upper or lower or no change) (2) , features you need or remove from output file(3,4,5).


2. Sequence Format Converter : This server for sequence file conversion is hosted by NCBI and utilize the Seqret of EMBOSS package to change the format of sequence files. Along with plethora of option of input and output file format, you can get the option for case change of sequence, reverse complement also on this sequence format convertor bioinformatic server

3. fmtseq: A BioSeq File Format Converter : JAVA is essential for the functioning of this sequence format converter. It have good capacity of sequence file conversion.                                      

4. Sequence conversion : it's a simple one to one file format converter program but have more than 50 file format conversion capacity 




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2 comments:

  1. LynnDecember 12, 2013 at 6:48 AM

    Hi.

    I'm Lyn from Malaysia. I'm doing bioinformatic for my postgraduate study. I'm having problem to convert .bcf file to .vcf file. I don't know how to convert the file.
    For your information, I'm using SAMtools for variant calling. My samples are blood and I'm going to detect novel SNPs. My pipeline get stuck at the file conversion part.

    I hope you can help me figure out this problem.

    Thank you and have a good day ahead.

    ReplyDelete
    Replies
    1. Priyanka PaulJanuary 14, 2014 at 11:52 PM

      Hi Lyn, As much I know you can use SAMtools to convert .bcf file to .vcf

      Delete

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