This program removes the sequences from the query fasta file that are present in a reference fasta file (removes even those query sequences that are present as substring in reference fasta file).

EXAMPLE:

Ref sequences:

>reference_seq_1

TSLDKDHLELCCTLSLPFSWACSWVLVLRLSINGQLPRSRLWAAHCLWGVP

>reference_seq_2

RGLCISGLEKEVQVQSRQAEGPVHLWLRKGSTSAE

Query Sequences:

>query_seq_1

TKTILNYAVLSPCLSPGHVLGC

>query_seq_2

LDKDHLELCCTLSLPFSWACSWVLVL

>query_seq_3

LWGVPRGLCISG

Output Sequences:

>query_seq_1

TKTILNYAVLSPCLSPGHVLGC

>query_seq_3

LWGVPRGLCISG

Output Sequence file will have only query_seq_1 and query_seq_3. query_seq_2 is removed because query_seq_2's sequence "LDKDHLELCCTLSLPFSWACSWVLVL" is present as substring in reference_seq_1's sequence "TSLDKDHLELCCTLSLPFSWACSWVLVLRLSINGQLPRSRLWAAHCLWGVP".