HaploSNPer is a flexible tool. It can be used in three ways.

1. Users can input a (Fasta) sequence as the seed sequence and select a corresponding database as target. Sequences homologous to the seed sequence will be obtained from the selected database. Haplotypes and SNPs will be identified in the extracted sequence dataset that contains the seed sequence and its homologs.

2. Users can input a seed sequence and other similar/homologous sequences at the same time. This is especially useful when users want homologous sequences to be part of the SNP search that are not yet available in (public) databases. These sequences and the seed sequence will be merged with the homologous sequences from the selected database, and haplotypes and SNPs will be detected in the merged dataset.

3. HaploSNPer can process a dataset containing a number of homologous sequences submitted by the user without specifying a sequence database. The dataset should be submitted at the "other similar sequence" option. Haplotypes and SNPs will be detected in this dataset only.

The seed sequence is either submitted in the seed sequence text area or uploaded from a file (the left part of the input option). Other similar sequences are either submitted in the other similar sequences text area or uploaded from a file (the right part of the input option). All sequences must be in FASTA format(see example).

Note:
1. If the total number of sequences (homologous sequences obtained from the selected database and sequences users submitted) for SNP detection is more than the threshold (100 for human and mouse databases,and 200 for other databases), an email address is required to send the results since the process may take some time. If the user submits an email address before submitting a job, the results will be sent to the email address by email irrespective of the size of the dataset.
2. When human and mouse database is selected, it is better to put your email there since it takes some time to search such large databases; and then the results will be sent to you by email soon.