Overlap Graphs test | Python Fiddle

def overlap_graphs(dnas, q):
    prefs = {}
    sufs = {}
    result = []
    l = len(dnas)
    for i in range(0, l):
        dna = dnas[i][1]
        dlen = len(dna)
        pref = dna[0:q]
        suf = dna[dlen-q:dlen]
        # Поиск не связан ли узел с другими ->
        for r_rel in prefs[suf]:
            result.append(dna, dnas[r_rel])
        # Поиск не связаны ли другие с ним
        for r_rel in sufs[pref]:
            result.append(dnas[r_rel], dna)
        #Добавляем в список суфиксов
        sufs[suf].append(i);
        prefs[pref].append(i);
    return result

def parse_input(s):
    lines = s.split()
    result = []
    cur_name = ''
    for line in lines:
        # Новая строка
        if line[0]=='>':
            # Проверка предыдущей строки
            if cur_name <> '':
                result.append([cur_name, cur_line])
            # Начало формирования новой строки
            cur_name = line[1:]
            cur_line = ''
        else:
            cur_line += line    
    result.append([cur_name, cur_line])
    return result
    
    
lns = parse_input('''>Rosalind_0498
AAATAAA
>Rosalind_2391
AAATTTT
>Rosalind_2323
TTTTCCC
>Rosalind_0442
AAATCCC
>Rosalind_5013
GGGTGGG''')

print lns
print overlap_graphs(lns, 3)

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