Find Chimeras - Inputs:

1. Sequence type:

   Select the type of sequences being input. Short length sequences are those less than 1,000 nucleotides, while Full length refers to sequences longer than 1,000 nucleotides. Short length sequences that have been assembled into full length sequences should be submitted as full length sequences. This selection is used to determine the optimal parameters for detecting chimeras.

2. FASTA File:

   Choose a text file containing the sequence records where you wish to look for chimeras. Here are some remarks on the input file:

   • Sequences must be in FASTA format where each new sequence record begins with a ">" symbol on a single line containing the description, and subsequent lines contain the actual sequence (there are no restrictions on the number of nucleotides per line).
   • Sequences can be aligned (with gaps) or unaligned (without gaps). DECIPHER will remove gaps from a sequence before running the Find Chimeras algorithm.
   • The size of the uploaded file is restricted to be less than 50 MB. This limit corresponds to roughly 32,500 nearly full length (≥ 1,200 nucleotide) sequences without gaps, but gaps in alignment files can reduce this number significantly. Therefore, we recommend that users upload unaligned (de-gapped) sequences to maximize the number of sequences that they can test at a time. The number of short reads that can be processed in each job is much higher: about 350,000 sequences of length 100 nucleotides, or 100,000 sequences averaging 500 nucleotides.
     
     To analyze more than 50MB of sequences, feel free to submit multiple jobs or download DECIPHER for use on your computer. However, we ask that you please submit no more than 4 sequence files at a time, and wait to receive the results before submitting more files.
   • Only sequences in 5' to 3' direction of the same strand will receive correct results. The following ambiguity codes are accepted:
     
     

     Symbol	Meaning
     A	Adenine
     C	Cytosine
     G	Guanine
     T	Thymine
     U	Uracil
     M	A or C
     R	A or G
     W	A or T
     S	C or G
     Y	C or T
     K	G or T
     V	A or C or G
     H	A or C or T
     D	A or G or T
     B	C or G or T
     N	A or C or G or T