Experimental evidence suggests that half or more of the mammalian transcriptome 
consists of noncoding RNA. Noncoding RNAs are divided into short noncoding RNAs 
(including microRNAs) and long noncoding RNAs (lncRNAs). We defined 
complementary DNAs (cDNAs) lacking any positive-strand open reading frames 
(ORFs) longer than 30 amino acids, as well as cDNAs lacking any evidence of 
interspecies conservation of their longer-than-30-amino acid ORFs, as noncoding. 
We have identified 5446 lncRNA genes in the human genome from approximately 
24,000 full-length cDNAs, using our new ORF-prediction pipeline. We combined 
them nonredundantly with lncRNAs from four published sources to derive 6736 
lncRNA genes. In an effort to distinguish standalone and antisense lncRNA genes 
from database artifacts, we stratified our catalog of lncRNAs according to the 
distance between each lncRNA gene candidate and its nearest known protein-coding 
gene. We concurrently examined the protein-coding capacity of known genes 
overlapping with lncRNAs. Remarkably, 62% of known genes with "hypothetical 
protein" names actually lacked protein-coding capacity. This study has greatly 
expanded the known human lncRNA catalog, increased its accuracy through manual 
annotation of cDNA-to-genome alignments, and revealed that a large set of 
hypothetical-protein genes in GenBank lacks protein-coding capacity. In 
addition, we have developed, independently of existing NCBI tools, command-line 
programs with high-throughput ORF-finding and BLASTP-parsing functionality, 
suitable for future automated assessments of protein-coding capacity of novel 
transcripts.