Table 1.

Remaining gap filling

Procedure: gap filling
Input: related contigs with remaining gaps
Output: related contigs
Step 1: prepare the query sequence;
Step 2: “setup”, specify related options and database, create a lookup table;
Step 3: “BLASTN search”;
Step 4: “back-track”, input the preliminary matches and locate the insertions and deletions of uncertain sequences;
Step 5: output the results in a file;
Step 6: Phrap software assembles these alignments